On a forested planet, Ronon Dex and Teyla Emmagan are talking about how Kanaan has been released from his prison camp on the mainland of M35-117 and has integrated in Atlantis.

They discuss that Kanaan had a scare with the city’s showers, and that Ronon offered to spar with him. Teyla then talks about Ronon, who recently stunned Doctor Garrett on his own surprise birthday. Their conversation ends, when they notice a black cloaked figure lying on the floor. The two tries to help, but Ronon inadvertently steps on a trip wire, which detonates an explosive. The hood figure stands up and fires a Wraith handblaster at Ronon, and shoots him three times before he succumbs to the stunner. Teyla looks at the assailant, who unveils himself. It is Tyre, who doesn’t look well. He later stuns her.

She later returns to Atlantis in the conference room with Lieutenant Colonel John Sheppard, Doctor Rodney McKay and Richard Woolsey. He tells them that the Daedalus could not detect Ronon’s subcutaeneous transmitter anywhere on the planet. They believe that Tyre has moved him, but think that he is not acting straight, since nothing would stop him from killing Teyla. They believe he may have kept some of the Satedan sense of honour. They discuss what their next move would be, Teyla suggests looking for another Satedan, and she knows just the one, Solen Sincha, on the planet Belkan. Woolsey commissions the mission to Belkan, and wonders whether Teyla decides to rejoin Sheppard’s team, since she hasn’t said anything official yet. Teyla says she hasn’t decided, but wishes to join the team for the mission. As they leave, the doors close. Woolsey prepares to leave, but the doors wouldn’t budge, much to his surprise.

On another world, Ronon wakes up tied to a chair. Tyre is next to him and tells him that they are in Sarif Sur, a planet where Tyre almost died in a mission. He then tells Ronon that if he joined them in the first place, Ara and Rakai may still be alive today. Ronon wouldn’t listen to him, but notices that his hands are shaking. Meanwhile, on Belkan, Sheppard’s team finds Solen in a tavern, who is evidently drunk. They confront him and tells him that Ronon is in trouble, which Solen points out “he’s always in trouble”. When he hears of Tyre, he tells them that he was a Wraith worshipper, since he disappointed the Wraith, they let him go. This was not an act of kindness, since they serve as a example to those who betray the Wraith, and he would be an easy target for all the Humans in the galaxy. He does however agree to send a message to Atlantis when he finds a lead.

On Sarif Sur, Ronon tells Tyre that he doesn’t look well. He tells Ronon that after their last encounter, the Wraith was disappointed by him and decided to let him loose. However, due to the Wraith enzyme he was used to receiving for the Gift of Life, he has gotten addicted to it, and after not getting more in a while, starts to get into withdrawal. Ronon, agrees to take him to Atlantis so that medical personnel could help him. However, he had his own intentions, he called for his own help. By capturing him, he alerted the Wraith to the planet, and with Ronon captured, Tyre would be saved again. A Wraith Commander enters the building, where he says he will be looking forward to Ronon serving him, before he quickly feeds on him.

Back in Atlantis, Woolsey and Teyla both talk about her future with the team. Woolsey respects her decision to take more time to think, even by offering a substitute for her for now. Teyla wonders if he has children. Woolsey hasn’t but once had a pet Yorkie, until his wife took him after their divorce. On Sarif Sur, the Commander, who has fed on Ronon, gives his lifeforce back. Ronon says he’ll die before he will submit to the Wraith. The Commander keeps trying. In Atlantis, McKay and Sheppard talk in the mess hall about how ro find Ronon. McKay tells him that he thought of everything, and even took the Archimedes approach by bathing for his “eureka moment”, but there is still nothing. As McKay talks further, Major Evan Lorne interrupts them and says that Solen has contacted them on the lead, a planet called Sarif Sur. They plan to launch a mission as they speak.

On Sarif Sur, Tyre begs Ronon not to delay the inevitable, and join him. Ronon refuses and still brands Tyre as a traitor to him and his people. The Commander enters and tells them that things are progressing slowly. They plan to move. Tyre wants the Wraith to take him back, as they originally agreed. However, the Commander goes back on the deal, and throws Tyre onto a wall, and leaves him to die before leaving with Ronon and the warriors. Sometime after, Sheppard and Lorne’s team arrive in the abandoned village and searches it. They find nothing, until Lorne finds Tyre unconscious. With his pulse weakening. They send him back to Atlantis, where Jennifer Keller tells them that he is going through Wraith enzyme withdrawal, and even broke his restraints to injure the guards. Keller could give him sedatives to ease the withdrawal, but will prolong it. They have to make his detox as quickly as possible. Meanwhile, Ronon and the Commander arrive in a Wraith lab. Ronon tells him he’d rather die, like Morika and Hemi. However, the Commander tells him that they didn’t die because they refused to join. They died because they were too weak to survive the process, but Ronon is strong enough, and will submit eventually.

For several days, Tyre continues his brutal withdrawal, while the Wraith Commander continuously feeds on Ronon, and takes his left back. Teyla and Kanaan, who is now back as a Human look after Torren John Emmagan. Kanaan tells Teyla that he’ll respect whatever decision she makes, since she has both the duty to look after Torren, and the people in Pegasus. Tyre finally recovers his withdrawal, and talks with Sheppard. He tells him that not only will he give him the location of where Ronon is being help, but will join them in finding him. Woolsey agrees to this. Teyla gives him Torren for him to take to Kanaan in the cafeteria, before she joins in on the mission, in the hopes of saving Ronon. However, it is too late. Ronon cracks, and is turned into a Wraith worshipper, who is told that Atlantis is his enemy.

Sheppard and Lorne’s team, and Tyre enters the facility, and kills several Wraith warriors. The teams enters a power relay chamber, where Tyre tells the teams to plant C-4 into the key sections and hide them, so that when it detonates, the secondary explosions will destroy the base. After they do that, they carry on searching the labs, when they find Ronon, who is expecting them, but the teams looks suspicious. Their suspicions are correct, when they find he is now working for the Wraith, as they were soon surrounded by several warriors. The Commander arrives to take the teams. Tyre then holds Teyla hostage, revealing he has double crossed the teams to take them prisoner, so he could rejoin the Wraith cause, which the Commander grants.

After being taken prisoner, Tyre and Ronon convince the Commander that the teams are more valuable alive and turn to worshippers. As the team are in the cells, McKay plans to talk to Ronon to appeal to him, since he is still a new worshipper. Next, Tyre comes up to Sheppard, and informs him that he has been summoned to the Commander. On the way, Tyre excuses the warrior, while they both take a decoy. Afterwards, they both meet the Commander, with Ronon next to him. The Commander decides that Sheppard would be perfect for the cause and attempts to convert him. He takes out his hand, and is about to feed on Sheppard, when Tyre quickly takes out his sword, and cuts the Commander’s hand off.

Tyre actually freed the teams and gave them their weapons back. Sheppard takes out two sidearms and kills the Wraith trying to get into the room. Tyre and Ronon engage in a sword fight. Ronon, who is stronger gains the upper hand and is starting to beat him to death, when Teyla and the team arrives and stuns Ronon three times, which takes him down. Tyre threatens the Commander to come with them, by threatening to blow the facility. Just as they made a break for it, the teams were once again surrounded. The Commander tells them to stand down and let them free. He wants to know what will stop them from blowing the facility anyway. Tyre takes the detonation device, and tells him that when the teams are free, he will hand him the device, before he can walk free. As the teams head back to the Puddle Jumper, Tyre gives his sword to Sheppard, signifying he intends not to follow them. The teams escape, and radios Tyre.

The Commander tells Tyre he is not beyond forgiveness, and it is not too late for him. However, Tyre says it is, for both of them, and detonates the C-4. The facility is destroyed, and the Jumper narrowly misses the explosion, which kills everyone within, including Tyre and the Commander.

Ronon is sent to the infirmary, where he is to go through withdrawal, but Ronon doesn’t give in easily, urging Sheppard to let him free or kill him. However, Sheppard leaves and allows Ronon’s brutal withdrawal, which takes several days. The teams could barely watch him, as he begs them to kill him. But eventually, he fully recovers, and tells McKay, who is with talking about his piano to get him some food. Ronon still has to stay off duty for a few more days to make sure.

Later, Teyla visits Woolsey’s quarters, who is drinking wine, listening to classical music and wears his suit for the first time since his transfer to Atlantis, since he feels the suit is the most comfortable set of clothing for him. She informs Woolsey that she has decided to rejoin Sheppard’s team. After the news, Woolsey wishes her goodnight, before she joins Kanaan and Torren. McKay is taking a bath in his quarters, where he gets a sudden idea, like Archimedes. Sheppard visits Ronon in the Infirmary and gives him Tyre’s sword and departs. Ronon stares at the sword for a few moments, and begins to mourn Tyre, who in the end considered him a friend.

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Teyla Emmagan is walking with her new born son, Torren John Emmagan, who is asleep, but in order to do so, Teyla would have to walk while holding him. She passes a tired Doctor Jennifer Keller in the infirmary, where she is looking through Michael’s database for the cure on Carson Beckett’s condition, and thinks she may have found something.

Teyla came to thank her for reverting the Hybrids back to Humans, and she had a chance to see Kanaan earlier today. Keller tells Teyla that Rodney McKay often talks with Beckett in the stasis pod, telling him of the latest news. Keller once caught McKay, who was then pretending to look over the systems. Torren starts to wake up, and Teyla gets moving again.

Meanwhile, in the control room, McKay, Lieutenant Colonel John Sheppard and a team await for Richard Woolsey’s arrival. He is then beamed down from the Daedalus. However, instead of a speech, he asks for his belongings to be sent to his quarters, and orders McKay to send him his latest reports. Sheppard sarcastically comments on his “nice speech” to the team, before going his own way. At night, Keller has fallen asleep, and wakes up. As she gets up, she notices that her right hand is covered a mysterious gelatinous goo. In horror, she quickly gets up and washes it away. She decides to turn in and sleep in her quarters.

The next morning, the team, apart from Woolsey enters the conference room, where they quickly notice that the table is replaced by a twelve foot long mahogany one. The team thinks why Samantha Carter was relieved of her command, since she has done exceptional work with the destruction of the Asurans, and the weakening of the Wraith. Sheppard thinks that is the problem. Since much of the threat has disappeared, the IOA felt to be put in control, since the threat level of the galaxy has gone down. Essentially, Carter has become a victim of her own success. Woolsey enters the room, and tells everyone to be seated. The group discuss several topics, including the events over M2S-445. However, all but Woolsey know that Michael may have escaped through the Puddle Jumper that went missing, and one of his ex-mercenaries reported to have seen him after his cruiser was destroyed. Woolsey deems the source too unreliable, and moves on to the next topic; the former Hybrids. Despite Teyla telling him that they are actually victims, Woolsey says they were also enemy combatants, and are to be held on the mainland until he deems them trustworthy to roam around.

The final topic is the status of the clone of Beckett in the stasis pod. A distracted Keller tells him that she thinks she has found a serum that can stop his cellular degeneration. Unfortunately, it has only been tested on lone cells, not a live person. The only way to test it is to put Carson out of stasis and inject him with the serum. Despite the risk that Carson may die the second he exits stasis, they go ahead with the procedure. They enter the stasis room, and deactivates the stasis field, where Beckett falls into the gurney. Keller quickly injects him with the serum, and sends him to the infirmary. They wait, when Beckett eventually wakes up. He sees his team again. Keller reports some good news; there are no signs of cellular degeneration, he’s in the clear. By the end of the day, Keller goes to her quarters to get some sleep.

The next morning, Beckett takes the opportunity to look at the city skyline. McKay confronts him and tells him that they plan to send him back to Earth to recover from his condition. Beckett seems fine with it, believing that he is still some time away from being in top shape again. They are then interrupted by Teyla from the headset. She wants their help. She tells the two that she went to Keller for a breakfast date, but couldn’t get an answer. She assumed she was still asleep, and now she is late for her shift. McKay manages to open the door, where they see Keller asleep, with no sign of her waking up. Teyla notices something, and pulls out the bed covers and is shocked at what they see, tendrils covering her stomach.

Sheppard and Woolsey is called into the situation. Beckett says that he saw this once before, when he was Michael’s prisoner. They move both her and the bed, since the tendrils are attached to the bed as well. They discover that the tendrils are actually growing from inside her. Woolsey lets Beckett stay, despite being scheduled for Earth, and that he is not an active expedition member, but has more experience in Michael’s experiments. Sheppard tells Woolsey that this “isn’t by the book”. Woolsey tells him that they must not get used to it. Beckett operates on Keller, and cuts off a small tendril. Unfortunately, her vitals shut down. The surgical team try their best to revive Keller, which they did. Beckett tells the team that he will not attempt that again, since it may kill her. Beckett takes a blood sample and discovers that she has been infected by a Wraith pathogen. Later, Keller eventually wakes up.

McKay enters the isolation room in a HAZMAT suit, and discovers that the mass has multiplied in size. Keller is visible afraid, and can’t go to sleep, through fear of not waking up again. She experiences numbness all over her body, and hears mysterious voices, which are most likely in her head. Beckett tests the blood samples on everyone that has been in M2S-445, and discovers they are all infected with the pathogen. The infected members are restricted to quarters, and Carter has been quarantined in Stargate Command. Woolsey still has not decided what to do with Keller.

Beckett finds out what the pathogen does, and presents his findings to Woolsey. The pathogen is comprised of a organo-metallic polymer, which overtime, will go hard enough to resist hyperspace radiation, and the material is similar to that of Wraith spaceships, meaning that a Hive Ship is most likely coming out of Keller. Due to this new threat, Woolsey orders the entire tower Keller is in evacuated. Another problem is that the tendrils are growing very rapidly. Teyla talks to McKay, who figures out the the tendrils are growing to get access to more power, where it well go too quick to stop it. He believes the tendrils are heading for a power source, a power conduit leading directly to the ZPM. Teyla tells this to Woolsey, who assembles a team to examine the advancing tendrils. Beckett also starts work on how to stop the pathogen.

Radek Zelenka, Teyla and a team are investigating the area, and Zelenka splits off from the team and watches the tendrils attached to a wall, that has attached itself onto the power conduit. As Teyla is coming, the tendrils sense Zelenka’s presence and attacks him, knocking him to the floor. Just as he is overwhelmed, Teyla fires her P90 onto the tendrils, which are retreating. She takes Radek to safety. With this information, Woolsey decides to have Keller terminated. Fortunately, Beckett invents the serum, a phage, which should kill the pathogen. The downside is, there is no way to test it. Sheppard volunteers to be tested first. He is restrained on a bed if anything happens. He is injected with the phage. At first, he doesn’t feel anything, but soon starts to violently convulse. Eventually, it stops, and Sheppard returns to normal, with the pathogen completely gone.

Woolsey decides to break the rules again, and decides to send someone to the isolation room to inject Keller. Unfortunately, there are several tendrils in the way. Ronon Dex volunteers, since he is infected, the pathogen in Keller would detect no threat from him. Ronon takes the phage with him, and starts his move. He goes into a transporter. The second he enters another section, the ZPM is pulled, blacking out the city. Ronon walks past the tendrils with no sign of being harmed. He then encounters a shell in front of him. With no other way, Ronon decides to shoot his way through, against Beckett’s wishes. He shoots through the shell, where the tendrils detect that he is a threat. He uses his sword, but is stopped and pinned down to a wall, where they start to strangle him.

With the plan going awry, Sheppard makes contact with Keller. However, he hears a more deeper-alien version of Keller’s voice. She tells him that she is not Keller any more, and when she is completed, she will have her own designation. Sheppard gets the team to buy time, so he could fly a Jumper. He flies it and sees that the entire tower Keller is in is completely covered in the mass. In a daring course, Sheppard flies the jumper straight into the tower and crashes. He arrives just outside the isolation room. He arms himself and makes his move. He quickly moves into the room, and injects Keller with the phage. Keller quickly wakes up in pain, and the tendrils eventually loses its hold of Ronon, who falls. However, as the mass dies, a tendril stabs Sheppard in the stomach. An injured Sheppard is about to kill Keller, until the tendrils stopped moving.

Sheppard is in the infirmary, recovering from his injury. Woolsey tells him that Ronon has a bruised larynx, meaning he will lose the ability to speak for several days. Sheppard comments “wonder if anyone’ll notice”. They then see Keller, who is now up and about, back to normal. Beckett arrives and says he is ready to go back to Earth and thanks Woolsey. He then talks to John and expresses his disappointment in himself for breaking at least half a dozen security protocols during his first week, but if he didn’t break them, Keller would be dead, and the city will be in serious trouble. His superiors at the IOA decide to let the matter drop. Woolsey firmly believes that the rules are “there for a reason”, and reveals that he is not sure if he is up to leading the expedition. Sheppard smiles and shakes his hand, where he welcomes him to the Pegasus Galaxy.

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On M4S-587, Lieutenant Colonel John Sheppard and Major Evan Lorne wait for their Genii contact, where he claims to have information regarding Teyla Emmagan, who was kidnapped by “Michael”.

However, the contact didn’t turn up, and decide whether the Genii are reliable, since they tried to have Harmony killed, but Ladon Radim didn’t order the hit, trying to get on their good side. With luck running out, Sheppard gates back to Atlantis, leaving Lorne to stay for a while in case the contact does show up. Sheppard returns to Atlantis. However, he notices something different; the city is empty, with no power on at all, as well as a glow of red from the daylight and the fact the temperature has raised. He calls for anyone, but has no answers. He then decides to look outside, but has trouble opening the door. When he is out, he sees that the oceans have mysteriously turned to desert.

Sheppard desperately tries to activate the city’s systems, but can’t. He then hears static, and hears a voice, Doctor Rodney McKay, who wants to know of Sheppard’s position, and what has happened. He then tells him to go to the Holo room. Sheppard runs to the Holo room, and activates the projector, where an aged McKay materializes, who is powered by a Mark XII naquadah generator, which is tapped into the city’s internal sensors. He tells Sheppard that he is a hologram of himself from 25 years since Sheppard was missing. He also relates that Sheppard was involved in a freak accident involving a solar flare, similar to the one where SG-1 was transported to the year 1969, but instead of traveling back in time, he went forward in time, by 48,000 years, likely making Sheppard the last man alive in the Pegasus Galaxy.

Fortunately, the hologram of McKay didn’t just come to chat with Sheppard. Instead, he has a plan to send Sheppard back to 2008, by waiting for a similar solar flare to send him back. The problem is that he would have to placed in a stasis pod for at least another 800 years. This is the only chance, since if he returns later than two months since he was missing, it would be too late. McKay reveals that two months after Sheppard was missing, they announced him KIA and had a funeral, without Sheppard’s body. The team later received solid intelligence on one of Michael’s labs, where they finally found Teyla, who had delivered her baby, but was killed by Michael.

Michael then used the baby to perfect his Hybrids, and later administered the Hoffan drug on every single planet in Pegasus. The Atlantis Expedition, with their limited personnel attempted to lessen the mortality rate of the drug, but were unsuccessful. With the Wraith’s food supply tainted, their civil war went into full swing, and within a year, the Wraith were brought to their knees. Michael’s army captured a Hive Queen, where he told her that when he escaped from the Humans, he expected a warm welcome back, but was met with scorn instead. With his anger, he personally decapitated her and showed her head to his army.

Now that Sheppard is aware of the situation, he realizes that if he rescues Teyla, he can stop all this from happening. However, on their way to the stasis room, he and McKay see the corridor is blocked off by a mountain of sand, and there is no other way out. The only other option is a trek across the sand to a nearby tower but Sheppard can’t walk across the sand due to a sandstorm that is raging outside. He decides to wait it out, while Holo-McKay tells him what happened to the others. He explains that with Michael in control of the galaxy, the IOA were hesitant in giving out resources to help stop him. However, Colonel Samantha Carter didn’t take no for an answer. They handed her a new Daedalus class ship, the Phoenix. Since it was barely off the assembly line, Carter, McKay and maybe Radek Zelenka, since McKay doesn’t remember, tirelessly helped finish installing the Asgard systems on the ship. After they were finished, Carter told McKay to return to Atlantis, while she would strike back at Michael.

Carter and the crew performed several guerrilla-style ambushes, where they would exit hyperspace, strike at Michael’s Hive Ships, and jump out again. Despite terrible odds, Carter inflicted considerable damage to Michael’s fleet. However their luck soon ran out. They found intel that Michael will strike at a planet, not knowing Michael’s army supplied Carter with misinformation. When the Phoenix arrived, the ship was ambushed, and several systems, including the Asgard plasma beam weapons went offline. The Phoenix fired conventional nuclear warheads, but did not cause much damage. With the ship’s hyperdrive and other engines reaching critical, Carter evacuated the entire crew. With the transporters down, Carter was left with little choice but to set a collision course for one of Michael’s Hives. The Phoenix charged into a Hive Ship, where the force of the explosion destroyed the other two attacking Hives.

Back in the alternate Atlantis, Holo McKay has discovered why the ocean turned to desert; the sun is dying, turning into a red giant, which will heat the planet so much, that in 500 years time, the planet would be so hot, the atmosphere will burn, which will kill Sheppard the second he exits stasis. Sheppard decides to use the city’s solar panels to power the shield (although most likely it was collapsed to protect only a small area) along with the naquadah generator, which will buy them enough time for Sheppard to return to the present. Then, since he can’t wait due to hunger, he covers his face and attempts his walk across the harsh desert. He pressures McKay to keep talking talking, by asking what happened to Ronon Dex.

After the death of Teyla and Carter, Ronon no longer felt welcome in Atlantis, and left. He learned that Michael was planning to convert the populations of the stronger worlds into Hybrids, and destroy the weaker civilization. Ronon planned and developed an army to take down Michael. With the galaxy in a state of panic, he didn’t have trouble in finding volunteers. The recruits were mainly farmers, but Ronon taught them every assault tactic he could. The Atlantis Expedition also supplied them with Earth weapons, particularly C-4 and P90s. After he felt his army was ready to fight, they embarked on several operations to take down the Hybrids.

In one particular mission, they attempted to destroy one of Michael’s labs. There, they ran into an old friend, “Todd”, who also planned to destroy the base. When they heard of Michael’s army zeroing in on the base, Ronon evacuates his army, while he and “Todd” use the C-4 to blow the base, but wishin toallow his forces to escape, the two hold off the Hybrids, until Ronon’s soldiers radio him that they have evacuated. With no way out, Ronon and “Todd” decided to detonate the C-4, where they shared a smile to each other, before Ronon detonated the explosives, killing them all, and destroying the base.

Sheppard, having survived the trek, is unconscious. After a whole night, he wakes up, and quickly agrees they should go to the stasis pod. They arrive in the stasis room, where Holo-McKay tells him to take a crystal, containing the address to the planet where Michael plans to kill Teyla. Before he steps in, Sheppard wants to know what happened to McKay. Jennifer Keller planed on a mission to help more lives in the galaxy, only to be stopped by the new Atlantis leader, Richard Woolsey. He told her that since Michael’s forces had taken over the galaxy, the IOA ordered all resources to be pulled for the protection of the city. Disgusted by this, Keller quits the Expedition. McKay decides to quit as well, and both leave on the Daedalus back to Earth.

During their time, the two grew closer and closer, until by the time they returned to Earth, they weren’t colleagues any more, and are seeing each other. Over the next year, McKay got a high paying job in an Aerospace engineering firm, while Keller headed her own practice. Things were fine between them, until Keller fell ill. When she turned to Stargate Command, the doctors discovered traces of the Hoffan drug in her systems, and told her that she was dying. With this, McKay had a revelation to prevent the whole thing from happening. However, Keller told him to stop, since there is no point in chasing after something that is already gone. She died three days later.

After 25 years, with help from his sister, Jeannie Miller, he finds a way, and presents the idea to Lorne, who was then a General in the SGC. He convinced Lorne to take him to Atlantis to enact his plan. After McKay finishes relating this, Sheppard enters stasis.

Back in the present, Atlantis’ Stargate activates, where Chuck reads Sheppard’s IDC. Sheppard returns, and discovers that he has returned after 12 days since he went missing. He tries to convince Carter of the news that he can find Teyla, but she find this far-fetched. When McKay notices the solar flare, they believe Sheppard is telling the truth. Carter sanctions the mission to M2S-445, the planet Michael is planning to kill Teyla. Lorne joins Sheppard’s team.

On M2S-445, the teams arrive in Michael’s base, where they split up. Sheppard and Ronon find a room, with several brutal surgical implements. Sheppard observes that this is the “sick, twisted version of a maternity ward”, which means this is the room where Michael plans to to both deliver the baby and kill Teyla. Meanwhile, McKay and Lorne enter another room, where McKay finds a relic computer. There, McKay discovers that the information is Michael’s database, containing his Hybrid research and planets where he is conducting the research. For a moment, the team is excited at the prospect of Michael’s downfall, until the computer shuts down, and a timer activates. The base is booby trapped, and while the teams desperately try to run, they are too late. The base collapses in on them, leaving the teams trapped.

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In Atlantis, Doctor Jennifer Keller and a medical team are examining Carson Beckett, a standard protocol Beckett helped to initialise, for people after being imprisoned by a large amount of time.

From the observation area, the team; Colonels Samantha Carter and John Sheppard, Doctor Rodney McKay and Ronon Dex wonder as to who they are seeing, since the Beckett they know was killed last year. Keller then finishes every test she thinks of, and confirms the fact that this man is Carson Beckett.

McKay visits Beckett in an isolation room and they both have a talk. McKay wants to know about what he went through. Beckett tells him of the events on M8G-352, when he was taken prisoner by Michael Kenmore. He remembers being injected with something, and then remembers waking up on another planet. Michael then told him to do some work for him, in working on the Hoffan drug and combining Human and Wraith DNA. At first, he refused to help, but one day, Michael showed him a young woman no more than 20 years old, and killed her in front of him in cold blood. After promising to kill more people like her, Beckett co-operated. He worked for two years, but never gave up hope on his team finding him. McKay then confessed to him they they weren’t looking for him, since he was rescued on M8G-352, and continued working for six months, until he was killed by an explosion. Beckett doesn’t take this news well.

Keller discovers the mystery of the two Becketts. She reports her findings to Carter. His telomeres, which are a part of a Human’s chromosome, which gradually shortens by the time the cell divides, has shrunk 30% more than they should for a man of Beckett’s age. This means that Beckett’s original cells has started degenerated when they were removed from the original Beckett, meaning the one they encounter is a clone. They tell the findings to Beckett, who also doesn’t take that news well, since he discovers that he came “out of a test tube”.

Meanwhile, Teyla Emmagan is being taken by Michael and some of the other Hybrids, including Kanaan on a planet that was culled by the Wraith, and abandoned by the survivors, making it the perfect hiding place for Michael to conduct his research. Teyla is taken to a room in the facility, where she finally reunites with the Athosians after six months. She sees Halling, and the two gesture the Athosian greeting. Teyla talks with them, who tells her that the night they disappeared, 50 men armed with Wraith stunners took them by surprise during the middle of the night, and there was nothing Teyla could’ve done even if she was there. Teyla told them they should not give up hope in the Expedition finding them, to which they reply by saying they held out the same hope in her rescuing her.

Carter and Sheppard’s team discusses their plans on Beckett. Despite no matter how willing he is to help, since he was created by Michael, he could lure the team to an ambush. However, they decide to let him help them. Out of all his time as prisoner, he only saw one Gate address, since they blindfolded him every time he was moved to another one of Michael’s facilities. The prepare for a mission. In the locker room, Beckett gears up, and tells Sheppard that he won’t regret this. The team arrive on the planet, and enters a crowded tavern. Sheppard questions the bartender, who tells him that no-one cares what they look for, so Sheppard offers him a deal. Ronon looks up at the balcony, and sees a darkened figure, who starts firing at them with the distinctive sound of P90 fire. In the process, the assailant kills the bartender, but is stunned by Ronon, but falls, injuring him.

They send the injured man to Atlantis to operate on him. There, Keller identifies the man, Nabel Golan. She, Beckett and a team works on operating on him. However, as Beckett gets some equipment, he suddenly collapses. As Carter and Sheppard discuss what has happened, McKay thinks that Nabel had the P90 from the weapons cache for the Athosians on New Athos. Later, they see Beckett recovering. Keller finds out that Beckett’s cells has started to degenerate due to the fact he’s a clone. They wonder why he is dying now and not two years ago. Beckett remembers getting an injection from Michael once a week, which stops his degeneration, and it now has been a week since his last injection, meaning his cells are degenerating. They both work on finding a way to reverse the effects, by trying to reverse engineer a drug by using the Ancient scans from his arrival. The two works together. At first, they lead to a dead end, but find a breakthrough, which leads in a dead end again. Keller suggests sending Carson into a stasis pod, which he quickly refuses.

In Michael’s facility, Teyla tries to talk with Kanaan to reach to him, but is unsuccessful, when he leaves. The next morning, Michael’s worshippers enters the Athosian room, and takes Teyla away. They take her to a table and restrained. She notices several chambers where several people are undergoing the process of converting to Hybrids. There, Kanaan guards her again. Teyla again attempts to reach out to him, and tells her that she will take all her people, and him out of the facility and into safety. Teyla successfully reaches out to him, as he now recognises her. After an emotional reunion, Kanaan tries to break her out. However, just as he continues, he stops, because Michael has entered the room. He excuses Kanaan, and starts to experiment on her. Teyla begs him not to harm her baby, which Michael says he wouldn’t dream of doing. Since the baby has the gift, like Kanaan and Teyla, but stronger. With the baby, he can perfect the Hybrids.

In Atlantis, Nabel regains consciousness, and notices Keller, which she doesn’t hide the fact that she originally didn’t want to save him. Nabel tells them that they know he’s been captured, since Michael has spies all over the galaxy, and would be killed if he talks. However, Sheppard suggests to give him asylum in another galaxy. He gives the team the location of where they’re keeping Teyla.

Beckett knows the layout of the facility, and shows it to the team. He volunteers to join them and storm the place. After he leaves, the rest of the team agrees that it wouldn’t matter if he leads them to an ambush or not. McKay chases Beckett, who collapses again, but regains his posture. McKay tells him that he doesn’t have to this and prove himself, but Beckett insists on staying with the team.

The teams arrive at the facility, and reads several lifesigns all over the facility, from both the Athosians, and mercenaries. Meanwhile, Michael closes down the conversion process of the people in chambers, which kills them. Teyla senses his fear, which he merely tells her that it is just concern. They plan to leave aboard his cruiser. As Sheppard’s team searches for the Athosians, they’re under fire from mercenaries, with Earth machine guns. Halling and the Athosians hear the gunfire, and after Sheppard’s team kills the two mercenaries, shouts out for help. Sheppard finally finds what is left of the Athosians, and lets them escape to the Stargate.

The teams search for Teyla and find a chamber where she was held. They are then pinned by more mercenaries. McKay then notices that a cruiser is charging its engines. Suddenly, Beckett leaves the team to try to rescue Teyla on his own. He finds the two men escorting Teyla, and kills them. Although she is surprised to see Beckett, she refuses to leave without Kanaan. Beckett attempts to convince her to come with him but is ultimately stopped by Michael. Beckett aims his weapon at Michael, where Teyla urges him to shoot Michael. However, Michael tells her that no matter how much Carson wants to kill him, his is unable to, due to the ability Michael has to mind-control any of his clones or hybrids. As Teyla reaches for the gun, Michael stops her and takes it. He tells Beckett that doesn’t have an injection for him, but tells him he served his purpose, before stunning him. Teyla is taken away.

McKay, Ronon and Sheppard discover gas canister behind the mercenaries, and shoots them, where they explode, so the team can kill them. They run towards Beckett’s direction and finds him, where he tells them that Michael has escaped with her. They hear his cruiser activates, and they rush to the outdoors, where they helplessly watches Michael’s cruiser taking off and escapes into space. Teyla is gone.

However, they don’t give up hope, since they have prisoners that will talk eventually. They also discover that Beckett has weakened so much, that any other collapses can be fatal. They talk him into going to stasis. They take him to a stasis room on a wheel chair, where a pod is ready. The entire team watches him pass them. Keller assures him that she has a whole team working on fixing him. He tells Carter to send his mother a message for him, with random thoughts. He passes Sheppard, who tells him that they’ll get him out in no time. Beckett tells him to find Teyla, which he will. He passes Ronon, who finally talks with him, saying he is afraid of this, and the two embrace.

Last, but not least, he talks with McKay, who tells him that he programmed dreams into stasis, where he can go fishing in the Scottish Highlands, with “blonde massage therapists”, which Beckett says he’ll do fine. McKay and Beckett agree that this is not goodbye, but merely, a “see you later”. He steps into the pod, where the field activates. Beckett is now in stasis, where the entire team still stays for a moment to say goodbye to him.

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Teyla Emmagan is in a forested world with Colonels Samantha Carter and John Sheppard, Doctor Rodney McKay and Ronon Dex, with a group of other people. There is also a pyre, with her baby’s father, Kanaan, who died of some unknown cause. Carter emphasizes that he would have made a good father. Teyla grabs a torch and starts to burn the pyre.

However, as it is set on fire, Kanaan suddenly opens his eyes, and yells Teyla for help. Teyla attempts to save him, but is stopped by Carter, who tells her that it is too late to do anything. Teyla watches in horror as Kanaan is being burned alive. Fortunately, these events did not happen, as it was just a nightmare. Teyla wakes up in shock.

Jennifer Keller is investigating a mysterious plague that has spread through seven planets. Sheppard then arrives and tells her and Carter that they just visited a world also hit by the plague, making the grand total of eight planets. Keller says that the plague is mysterious, as the planets hit by it has no contact with any other planets that are affected, and the infected worlds made contact with other planets that has not been hit with the plague, meaning that it is so random, Keller can’t determine the planet of origin. It also has a mortality rate of 30%, and after that, the sickness would have run its course. Despite the 30% mortality rate, around 200,000 people would still die from those planets.

Meanwhile, in the Atlantis mess hall, McKay joins Teyla, who wonders about Keller’s progress in the plague. Teyla then notices McKay holding something behind his back. He reveals it to her as a pre-baby present; an MP3 player, which contains some of McKay’s scientific theories, since he knows that on Earth, a company specializes on sound recordings for pregnant mothers listen to teach the fetus on certain areas, so if Teyla’s unborn son learns McKay’s theories, he could become a brilliant scientist. Teyla is grateful, but McKay couldn’t help notice Teyla is also hiding something. She confides in him that she had a dream last night, and thought it was a vision. A skeptic McKay tells her that he believes her, citing her time in the Battle of the Void, the Laura Cadman incident, and seeing himself from a Parallel Universe. He then talks with Sheppard, and tells him that he doubts she had a vision, thinking that the thought that the Athosians are gone for six months is really starting to get with her.

That evening, Teyla has another dream. She wakes up in a forest, and sees Kanaan materialize in front of her eyes. After a happy reunion, Kanaan asks her for help in finding him and the other Athosians. Teyla does not know where to begin, until Kanaan shows her a pendant she gave him once in the village of Croya, which gives her a clue on finding them. Teyla then wakes up, sitting up on her bed, with her hand out and open, as if she was living the dream.

After telling her team, the team, except for Teyla has a meeting with Carter. They tell her of M2S-181, a peaceful trading settlement, which they will find surprising if they had anything to do with the Athosians. But since it’s Teyla, and that they owe her one, they decide to send Teyla with them to the planet, since the rest of the teams are stretched thin with the plague. The team arrives in the village of Croya, where they warn Teyla that if anything happens, she will run for the gate, leaving the team to deal with the problem. However, as they enter the village to meet with the same artisan the Athosians bought the pendants and jewelry, they discover that he died during the “great sickness” (possibly the plague). After they search the village twice for any answers, the team has to leave and go back to Atlantis, putting Teyla in disappointment.

Meanwhile, Keller informs Carter that she found something for investigation; they have encountered something like this before. The protein markers are almost an exact match to the same drug created by the Hoffans, but a new and improved version, with a lesser mortality rate than 50%, like last time. When she reports the findings to the team, she tells them that the Hoffans must have distributed the drug without the Expedition’s consent. However, the Hoffans are not responsible, McKay tells them that when the Wraith found out what they were doing, the Hoffans were wiped out. Whoever was responsible, laced the drug into the planets’ food and water supply, and due to the random nature of it, the Wraith would have no idea which “meal” would become their last. Carter orders the team on a mission to Hoff to find what they can.

Teyla is in her quarters, meditating, where she has the dream again, only this time, she isn’t asleep. She sees Kanaan again, and tells her that she was so close to finding a clue, and wondered why she left too soon. He urges her to go back to Croya. Teyla later confronts Carter, and wants her to send her back to M2S-181, and this time, she won’t take no for an answer. She tells her that she and Kanaan both have the Gift, which they are able to communicate each other over a distance. Carter is convinced and has Major Evan Lorne and his team assist her, since she doesn’t want Teyla going alone. In the end, Carter tells Teyla to call her Sam.

Meanwhile, Sheppard and McKay arrive in the city on Hoff, except this time, the city is heavily damaged from a Wraith bombardment. McKay searches through a room which used to hold the repository of Hoffan knowledge, except the room has been ransacked, and there is no information on the Hoffan research. McKay then finds a group of scared children, running away. McKay stops one of them and wants an answer on what happened. The kid tells him that they found the place empty when they got here, before running away again. With nothing more to report, they return to Atlantis.

Lorne’s team and Teyla arrive on M2S-181 and starts searching for clues. This time, however, Teyla spots a merchant holding a necklace that looks familiar to her, Kanaan’s pendant. She confronts the merchant, and demands to know what else he received from the trader who gave her the pendant. She sees a box, containing a necklace from Balera, and a ring from Halling. The merchant tells her that the trader is more than likely going to pay him a visit today. Meanwhile, back in Atlantis, the team returns, where they find an activated Wraith tracker, and that it is from their “friend”, “Todd”, who wants to meet them, or just draws them to an ambush, so they Gate to the planet, much to McKay’s chargin, since he hasn’t had lunch yet.

On M2S-181, after waiting for some time, the merchant signals Lorne from a distance that the trader has arrived. The trader shows the merchant some more valuable merchandise. Lorne confronts the trader on the whereabouts of the merchandise. The trader attempts to flee, only to have Teyla hit him in the head with a log. They send him to a room and wakes him up. They press him for an answer on the whereabouts of his merchandise. He doesn’t co-operate, but decides to help after Teyla threatens him that she will tell the village that he is a Wraith worshipper, which they won’t take kindly to. The trader admits that he got the merchandise from a planet with a mass burial ground. He tells them that he didn’t take them from dead bodies, since he found a box instead with all the merchandise. He agrees to send the team to the planet.

McKay, Ronon and Sheppard finds “Todd” in a Wraith lab, where he tells them of the drug that makes the Wraith die if they feed on Humans. At first, “Todd” accuses them of unleashing the drug, until they tell him that they think he did it himself. If neither are responsible, “Todd” explains that there could only be “one other” who would be responsible, but wants a price on the information, the research into the Hoffan drug. Meanwhile, Lorne plans to Gate Atlantis first to inform them of the situation. However, a Wraith Dart approaches. The trader grabs hold of Teyla, and is beamed away.

Back in Atlantis, Carter decides whether to give “Todd” the information, but McKay says they can offer him something that in the long term, would lead to their downfall. The Gate activates, with Lorne’s team. They tell Carter that Teyla has been taken. Meanwhile, Teyla is imprisoned onboard a cruiser, and meets again with a familiar face; “Michael”. He admits to have been behind the plague the whole time, and that he rewrote his DNA to eliminate his feeding need, meaning he has turned into a Hybrid. He also admits to being responsible for the kidnapping of the Athosians, and turned Kanaan into a Hybrid. He also has plans for Teyla’s child. Before he leaves her, he explains that he had “help” in perfecting the Hoffan drug. While Teyla tries to get through to Kanaan, he merely says that their child would serve the cause.

Sheppard’s team approaches “Todd” that they already know who’s responsible, and gives him the research, in exchange for information to a relay outpost. After they returned, McKay finally eats some food, where the team learns that there is rumor from Wraith worshippers of a valuable prisoner coming towards a certain planet. They dispatch the Daedalus to the planet. Once they arrive, Sheppard and Lorne’s team are beamed down to a compound, and search for Teyla, only to be under fire from the worshippers. The teams fire back and takes down both of them.

Meanwhile, Michael’s cruiser arrives over the planet, detects the Daedalus and starts firing. The ship fires back and is planning to destroy it. Sheppard questions the surviving worshipper, and tells him where Teyla is. He tells him that he is too early. Sheppard radios Steven Caldwell and tells him that Teyla is on board. Caldwell then tries to only disable the cruiser. But before they could act on it, the cruiser jumps into hyperspace.

Meanwhile, Lorne and Sheppard are contemplating what the guards on the base were trying to keep them from. They encounter a locked door, and blows it open. When they enter, they aim their weapons, but quickly puts them down, much to their surprise on who is inside it; Carson Beckett, who just appears in front of them, where he wonders what took the teams so long.

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Teyla Emmagan has just returned from an interview with the IOA at Stargate Command. She tells Colonels Samantha Carter and John Sheppard of her harrowing experience, since she was warned about Mr. Coolidge, who was brusque and arrogant towards any alien members of the Stargate Programme.

She also tells them that he felt distracted with her pregnancy, and kept calling her “honey”. After she leaves, the two colonels are wondering what to do next, since Ronon Dex’s interview is next, and his temper could cause “tsunamis” against Coolidge. Carter however, has an idea. Since his interview is not for two days, she calls for some assistance to teach Ronon, Teal’c.

Carter welcomes him to Atlantis, and notices his change in hair style. After aweing at the site of the Ancient city, Teal’c finally meets Ronon, who is sparring with someone, and easily beats him. Carter introduces him to Teal’c to help him through the interview process. However, it is obvious that Ronon does not trust him, even after the two are left alone to become better acquainted.

Later, the two meet in the mess hall, where Ronon tells Teal’c that he has dealt with the IOA before, and knows how to handle interviews, despite Teal’c’s warnings that Coolidge is far less pleasant than Richard Woolsey. They then proceed to talk on other topics, namely what happened on Sateda several years ago. Ronon explains that his people never gave up in fighting them, and they all fought until they were all dead, or captured. When Teal’c accused him of leading the Wraith to Sateda, an angered Ronon stood up, and aimed his weapon point blank at Teal’c’s head. Teal’c tells him that this question would be what he will face in the upcoming interview, and trusts that Ronon won’t aim his gun next time. Sheppard comes in and orders Ronon to drop the gun. He then tells them to go to the gym and teach each other how to fight.

During their sparring session, they attract a large crowd, who are betting on who would win, since the two have been sparring for an hour, with no breaks, and no sign on who’s winning. Carter sees the brutal sparring match, where she decides to break it off, announcing the fight as a draw. Afterwards, both Ronon and Teal’c leaves Atlantis for the Midway space station to get to Earth. But before Ronon leaves, Sheppard tells him to just think of what Teal’c has said, since he is over a hundred years old, and knows how to handle himself. Meanwhile, as they leave, on an arid planet of M4F-788, a group of Wraith are preparing an attack somewhere.

Ronon and Teal’c arrive at the Midway station. Doctor Bill Lee is working with Scott Dempster and Peter Kavanagh on familiarising themselves on Midway’s systems. Lee greets Ronon and Teal’c and shows them their quarters, since they have to share. He also tells them of the 24 hour quarantine. As they enter the quarters, they both decide on taking the bottom bunk, before staring at each other.

Meanwhile, back in Atlantis Rodney McKay discovers that the Intergalactic Gate Bridge is down, and is working on restoring it. In horror, Sheppard thinks that Ronon and Teal’c have gated to one of the Spacegates and are dead in space. McKay assures him that the malfunction is coming from M4F-788, so in all likelihood, they are just stranded on that planet. However, they do not know that Wraith are there, and are actually Gating to the Midway station.

In Midway, Lee notices the unscheduled Pegasus activation, and only watches in horror, as the Wraith go through and stun the guards. Soon, they enter the room where he, Dempster and Kavanagh are in, and hold them. Meanwhile, Ronon and Teal’c are watching The Three Stooges on the TV, when they hear the alarm. When the two come to investigate, they notice the Wraith. Ronon kills two of them, and wonders what the Wraith are doing. Teal’c asks the same question and investigate further, and proceed to the armoury. The Wraith Commander orders one of his technicians to Gate to Earth, but there’s a problem, they cant access the Gate system because of a lock-out command. The technician tries to hack the code, but in order to reach the code faster, the Commander feeds on Dempster.

McKay is finally able to dial to M4F-788, because someone dialed out of 788’s gate to prevent them from dialling in. Sheppard thinks that if Ronon and Teal’c are in the planet, nothing will stop them from dialling back. They send a MALP to investigate the planet. At first, they find nothing, but as they pan left, they see a DHD with Wraith tech, and a Wraith Cruiser, before they destroy the MALP. They deduce that the Wraith have infiltrated the Midway station, and think that “Todd” is involved, since he had plenty of time to hacking into their computer systems while he was a prisoner. With the Daedalus out of reach, they decide to send a team to take back Midway, by gating to M6R-125, a planet near 788, so they could reconfigure the macro and then to the Midway station.

The Commander has fed on Dempster, who is now dead. He then plans on feeding on Kavanagh, who reacts by fainting. He then plans to feed on Lee instead, but is stopped when the technician hacked in, they can now Gate to Earth. In the SGC, their Gate dials, and Sergeant Walter Harriman receives Midway’s IDC, and opens the Iris. They then notice a big orbe going through. When it lands, the orb discharges a blue pulse wave, which knocks out everyone on the base. The Wraith now have control of the entire base.

Meanwhile, in the Midway station, Ronon and Teal’c see Wraith going through to Earth. They both decide to follow them and kill them all. As they approach the Gate, the Commander shuts it down, but the two have made it through. The two find the Wraith stun bomb, with several unconscious SFs, and no sign of the Wraith. In the control room, they find several Wraith through CCTV cameras, trying to break out. Teal’c notes that the Wraith device has effectively locked down the entire base, so no one gets out.

Sheppard, McKay and a strike team ready a strike to take back the base. In the station, the Wraith notices the Pegasus Gate activating. The Commander did not expect re-enforcements so soon, and sees Humans entering. Sheppard radios Ronon and Teal’c not realising they are actually stopping Wraith in the SGC. Sheppard’s team is cornered by Wraith, but they open fire and are eventually able to kill them all. A screen activates in front of Sheppard, revealing the commander. He confirms to Sheppard that he got the information from “Todd” all along. The Commander doesn’t take Sheppard’s threat kindly, and responds by sending in the second wave. Sheppard tells the marines to guard the gate and kill anything going through, while he, McKay and two marines make it to the control room, where they killed the Wraith, but the Commander has disappeared. Lee and Kavanagh are rescued. Unfortunately, they can’t close the Stargate, and more Wraith are infiltrating the facility.

Back in the SGC, Ronon notices Teal’c says “indeed” a lot, which Teal’c says that has not noticed. They then find several Wraith, and kills them all. In the process, Ronon gets into a struggle with one, but is killed by Teal’c firing Ronon’s weapon. He shows a great interest in obtaining one. They then pass a room, and hear a noise. They investigate and finds Coolidge, who has regained consciousness. He tells both of them to send him to a radio for assistance when he learns of the Wraith incursion and that the two “aliens” are the only two dispatching them. On the way, the trio encounter more Wraith, and shoots and kills them all, but Coolidge has fled due to the gunfire, and his fear. The two split up to find him.

Kavanagh regains consciousness and is able to shut down the Gate by using the critical systems bypass. However, McKay tells him that the Wraith have tampered with that idea, sabotaging it so that shutting down the gate initiates Midway’s self-destruct, with 10 minutes until the station blows up. McKay radios Sheppard, who tells them that there is a Puddle Jumper in case of an emergency such as this. They plan to evacuate, but Wraith are surrounding the control room. Sheppard finds more Wraith and kills some of them, before he is outnumbered and retreats. When the marine team is overrun by the incoming Wraith (and presumed dead), Sheppard tells McKay to vent the station’s atmosphere, which McKay reluctantly agrees to. McKay starts venting the station, and Sheppard tries to find safety. However, as he is about to, the Commander shows up and they get into a struggle. Sheppard manages to get his sidearm and kills him. Unfortunately, with most of the air gone, Sheppard struggles to stand up and continue.

In the SGC control room, Ronon finds Coolidge, who has contacted the military, who has been ordered to nuke the base, which he won’t abort until every Wraith is dead. He also wants Ronon and the group, who has just awakened to escape in an escape hatch. However, Ronon sees Teal’c in trouble and goes to his assistance, against Coolidge’s wishes. Ronon rushes to Teal’c’s aid, and fights off some of the Wraith. He takes out a pipe and kills one of the warriors. Teal’c loses a battle and is pushed to the wall, where the Wraith starts to feed on him, but a few seconds later, Ronon jams the pipe through the Wraith, killing him. They now both believe that all the Wraith in the base are dead.

In Midway, McKay repressurizes the base, as all the Wraith are now dead from lack of oxygen. The team runs to the escape pod modified Jumper, but on the way, McKay hears breathing noises from one of the space suits. It is Sheppard, who has hid in one to save himself on. They both enter the Jumper, where the team are surprised to see Sheppard alive. With just seconds to go, Sheppard pilots the Jumper and flies out before the base is destroyed.

In the SGC, now the Wraith threat has disappeared, Ronon goes for his interview. Coolidge asks him if he feels he can fulfill the duties of an SG team member with diligence, integrity, and respect for those in authority over him. When Ronon says yes, Coolidge looks at the fellow IOA members, then merely says “good enough for me”. With the interview over, Ronon tells Teal’c that the IOA committee said he is everything they’re looking for, and that he didn’t threaten them with his weapon. Now that events have finished, Ronon is beamed aboard to the Daedalus to check out the status of the Midway station which has not responded to any communications since the attack began.

About a week or two later, the Jumper is still drifting in the massive void between the two galaxies, where Lee and Kavanagh argue about the movie “Pearl Harbour”, which Kavanagh likes. McKay snaps at them, and tells them that they never shut their mouths the entire time. The team then experience a shudder. The rear hatch opens, revealing Ronon, who tells them that they are onboard the Daedalus’ in the 302 bay. Ronon wonders where Sheppard is, since he didn’t hear the radio call. McKay opens the door to the front section, where McKay says that after just a day, he sealed himself in. Sheppard is asleep, wearing a pair of headphones. Ronon wakes him up, and tells him that the IOA has approved him for active duty. The Daedalus then jumps into hyperspace, heading back to Atlantis.

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Doctors Jennifer Keller and Rodney McKay report their findings of M5V-801 to Colonels Samantha Carter and John Sheppard. The planet has been suffering from tremors for several generations, and experience around four tremors a day, as the settlement is built over seismically unstable ground.

Also, it was a mining planet. Twenty years ago, the Genii came and forced all the inhabitants as miners for their own personal gain. However, after the Genii got the resources they needed, they abandoned the planet. Because of this, and the unsafe air quality, an abnormally high number of inhabitants are suffering from respiratory problems. They organise a mission to evacuate the settlement into another part of the continent, but in order to do so, the inhabitants have a list of demands a “mile and a half long”.

Carter arranges for her, Keller and McKay to the planet. An hour later, they arrive and are walking to the settlement, when McKay steps through a very weak, hollow part of the ground, which causes a hole in the ground, where McKay falls through it. Carter and Keller, lay on the ground to spread their body weight, and sees McKay at the bottom, hurt, but alive. However, as the women plan to dial the Stargate for help, the hole gets bigger, and they fall through also.

The trio find themselves in the abandoned Genii mining facility. Upon further investigation, they see a massive door, presumably the main entrance and exit. McKay notice a panel of Genii numerals, which requires a code to open the door. However, since they don’t know the code, they move on to the next sealed door, painted red, which most likely means the door was sealed for a reason. Their suspicions turn out to be correct, when they notice a very high drop down the chasm on the other end.

With nothing much more to do, they decide to just sit and wait for rescue to arrive, since if they don’t report to Atlantis, they’ll soon send help if anything goes awry. However, as they sit and wait, they experience a tremor, and notice the facility is starting to give way, since they facility is only supported by metal stilts, which are starting to give way, since the three people and the earth is putting on more weight for the complex to support. With this information, help may came too late, so they plan to escape. They notice a load of crates around. Their plan, is to stack the crates into a pyramid-like fashion. Meanwhile, in order to reduce weight, Keller removes the earth to down the chasm.

With the crate-pyramid, Carter starts going up the crates, since both McKay and Keller are both afraid of heights. However, as Carter approaches the top, the wood starts to crack below her and give way. However, so close to escape, Carter continues to reach the beams to the hole and climb up, but before she is able to do so, the crates shatter, and Carter slams into the ground on her stomach. Since that plan didn’t work, they have to think up a new plan.

Soon, McKay finds something to double up as a grappling hook. However, since they couldn’t find rope, McKay estimates since the hole is 20 to 25 feet high, and thinks that if they strap jackets, shirts and pants together, it could create a rope long enough. He tells them to strip, and Keller starts doing so, until Carter conveniently found rope. Keller then pulls her shirt down and replaces her jacket, while an obvious look of disappointment comes across McKay’s face. Carter notices the rope is too thin for them to grab onto, so she and Keller starts tying it. McKay reads through Genii files, hoping the files could contain the codes to unlock the door. Meanwhile, the women play “who would you rather”. There, McKay overhears the name Neil deGrasse Tyson, where he claims he once stole an idea from him. He is then forced to play the game with them.

Suddenly, they hear the noise of children playing in the field. Together, they all scream for their help. The children notice, and are just curious why the trio are down their. The trio ask them for their help. However, they say they can’t, because if their parents finds out that they are helping strangers in an area they’re not supposed to play in, they’ll all get into trouble. This angrily upsets McKay, but Carter attempts to bribe the kids by saying “We’ll get you what ever you want.” Knowing exactly what a pair of ten-year-old boys would want, McKay states that is brilliant and tells Carter to take her shirt off. Carter says “I think we can reason with them without going into that” and McKay turns to Keller, who says nothing and does nothing.

After the kids leave, the trio talk about Radek Zelenka, after Carter was trapped with him during the quarantine lockdown, and all agree that they find him weird. The women then wonders what happened between them and Katie Brown. He told her that he needed some time to figure out his emotional problems. However, Katie interpreted that as McKay breaking up with her and she has been put on the list for return to Earth. McKay assumes its for the best, but Keller thinks that she deserves to be with a nice guy like him. This seems to cheer McKay up. They then hear the kids returned, but just came here to win a bet with their friends. As McKay barks at them, another tremor strikes the area. They have to move fast, as the facility is becoming more unstable.

They finish with the rope, and McKay insists on throwing it through the whole. However several attempts later, McKay still can’t do it. One attempt hit a gas pipe, which ignites. Carter quickly stops it. Carter then has a go and succeeds in sending the rope through. Unfortunately, the hook just simply throws back, sending more earth in its path. With this plan in the toilet, McKay has another idea. Using the rope to the metal beams, they could make a bridge using planks to put up a crate on it, and climb to safety. However, there’s a problem, the planks aren’t long enough to make it from one metal beam to another.

Keller, however, has an idea on how to make it work, by a simple bar trick; they use three planks in a way that it could support the crates. Keller demonstrates with knives and cups in their packs. After the demonstration, they get on it. They line up the planks to form the bridge, and place a crate in the middle. Afterwards, Carter attempts to get on the crates, and manages to reach the hole, and is about to grab hold of it, when the bridge collapses. Carter falls 25 feet down and breaks a leg. As Keller tends to her, she finds out that she has about an hour until the internal bleeding could get severe.

McKay then has another idea on how to escape, by using the hook and rope option, except this time, they use the gas pipe. McKay constructs a cannon and fills it with some gas. He then places the rope on the cannon and then uses a detonator to ignite the gas. As Keller carefully aims it at the hole, the rope is fired out of the hole and catches some ground. McKay pulls the rope, so the hook can grip some land. However, the more he pulls, more earth is dropping down to the facility, gaining more weight. The facility’s metal stilts starts to buckle under the strain. Keller falls backwards through the red door and is falling. However, she has hold of the rope, and McKay tries to hold on, causing pain in his hands in the process.

As McKay tries to pull her up, Keller tells him to stop, since she can see light, a mine shaft coming out to the open. Keller is able to swing and makes it into the tunnel. However, this causes McKay’s hands to bleed. But he insists on taking Carter down, since her leg is broken. McKay makes a make-shift seat for her, and ropes her down, where she is able to swing to safety. Now she’s safe, it’s now McKay turn. He goes down, but pauses when it is time to swing. He admits that after four years of “shooting guns, running around, and saving people”, he should be better at it by now, but isn’t. He takes a break, when he feels the rope starts to snap. He swings and makes it to the tunnel with the women. Just after, they see the facility completely collapse, and falls down the chasm.

Carter, McKay and Keller make their way back to Atlantis. Keller tells McKay that he lost a bet with the bar trick and that he owes her a drink. However, McKay is oblivious to being asked out in this intimate moment. Which Keller asks him again, clarifying and they leave together.

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Lieutenant Colonel John Sheppard and Ronon Dex talk on one of Atlantis’ hallways, talking about a movie Ronon saw last night, “Blades of Glory”. He complains that the movie title is misleading, as there was barely any fighting in it.

When Sheppard explains that the movie was about ice-skating blades, Ronon tells John that “his planet’s weird”. John is about to enter his quarters, when she is stopped by Colonel Samantha Carter. She tells him that she received a communication from Stargate Command that his father, Patrick Sheppard just had a heart attack last night, and passed away because of it. Meanwhile, on Earth, in some facility, a woman is looking for intel on a certain thing, looking through satellites to do it. With her is some pictures of Sheppard and Ronon in Vancouver when Jeannie Miller was kidnapped. Her computer then finds something, a newspaper report about the death of Patrick Sheppard.

Sheppard is packing his bags to Gate back to Earth. Doctor Rodney McKay then visits him in his quarters, and tells him that he’s sorry about the loss. He also requested to join him, but the EM generator on M7G-677 is malfunctioning, and has to fix it from being attacked by the Wraith. Sheppard then goes to the Gate Room, where the Stargate is dialling. He is then joined by Ronon, who says he’s coming with him to Earth.

John and Ronon arrive in a big house to attend Patrick’s wake. There, Ronon realises that there are a lot of people attending, since Patrick was well connected. Sheppard meets his brother, Dave Sheppard, who has now taken over their father’s company. Dave and John agree that they should soon talk. Afterwards, John enters a room, where he sees his father’s coffin. Ronon picks up a plate and collects a lot of food from the tables. When he meets up with Sheppard again. He explains that the house was one of many houses he grew up in, and that his father pretty much arranged John’s life for him since he was fourteen, but they never talked again after Sheppard’s decision to join the Air Force. They are then met by Nancy, John’s ex-wife, who works at Homeland Security, and was recently promoted to director. Without realising, the same woman looking for them is also attending the wake.

When Ronon and Sheppard enter the bar, they are met by the woman, who identifies herself as Ava Dixon. She says she knows about the events of McKay and Miller’s kidnapping. At first, Sheppard attempts to tell her that he doesn’t know what she’s talking about, but tells her what she wants when she clearly knows too much. They need to talk, but not in the house. When they take her to the car, Dave stops them, and accuses Sheppard of challenging their father’s will. When John explains he has nothing to worry about, Dave tells him that his father regretted his son’s decision to break the contact with him to join the Air Force ever since, and wanted a chance for things not to end badly between them. Ronon, Sheppard and Ava then leaves.

At night, Ava explains to the men that Stanton Research, a division of Devlin Medical Technologies has worked with nanotechnology. She was recruited by Richard Poole, Stanton’s head scientist, and witnessed a major breakthrough she didn’t expect seeing in her lifetime, on an alleged government funded research called Project Archetype. However, she soon learned that the research was not sanctioned. They were able to make a person out of nanites, a Human form Replicator, even though replication isn’t one of its programmes. Three weeks ago, the IOA tracked them down, and attempted to stop them. Poole was planning to destroy the research and shut down the Replicator, but when it realised what Poole was up to, he attacked him, and killed two guards to escape. The Replicator is now loose on Earth, and she needs their help in tracking and stopping it.

Ronon and Sheppard storms the lab and arrests Poole, who is also trying to find the Replicator. They then beam him to the Apollo, where they interrogate him. He has heavily encrypted his files, which would take a long time in cracking, and only he needs the code. He refuses to co-operate, even after Sheppard agrees on a deal with him. Ava agrees on helping Sheppard track the Replicator, against Poole’s wishes. Sheppard and Ronon then meets with Bates, who was honorably discharged from the Marine Corps, and now works for the IOA field operations division. Next they see Bill Lee, who was interrupted from his first vacation in three years. Ava realises that the technology in the ship is alien. There, they track the Replicator’s signature to an old abandoned warehouse. The Replicator’s there because social interaction is not one of its programming, and will kill if he’s scared again. Sheppard talks with Poole again to track him down. At first, he doesn;t co-operate, since there will be no trial for him on what he knows. However, he changes his mind, when he threatens to lock up Ava.

At the warehouses, Poole tells everyone that the Replicator is immune to ARGs, and if they have to take it down, enough firepower and bullets would do it, since it has a limited ability to self repair. They then split up in teams to search the Replicator. Poole is with Bates. They see the Replicator, but after Bates informs Sheppard, Poole knocks him out and enters the warehouse alone. The Replicator comes out of hiding, where he tells it that he has to shut himself down like he has done several times, and assures him that he will re-activate him. However, the Replicator does not believe him, and kills him. Sheppard and Ronon finds Bates, and then finds Poole, dead.

As they exit the warehouse, they hear weapons fire and tracks it. There, they find the Replicator, and tries to kill it, but even with several armed men and several machine guns, they only caused minor damage. Eventually, the Replicator escapes, by jumping into a lake and the teams lost him.

Now it has disappered and they can’t find him, the team returns to the Apollo, and gives Ava the news, since her parents died very young and Poole was a father figure to her. Meanwhile, Lee can’t find the Replicator anywhere, even by boosting the sensitivity for energy signatures by 200%. They then wonder why Poole went by himself. They think that Poole has a buyer, most likely from the military. Meanwhile, Sheppard goes to Washington D.C. and encounters Nancy. He wants her to find out anything she can on Project Archetype. Nancy reluctantly agrees, after they argue about the time they were married, that Sheppard kept leaving her on top-secret missions around the World.

Later, Sheppard returns to the Apollo, where Lee is finally able to hack into Poole’s computer, and made a shocking discovery; Ava Dixon was actually killed in a car accident last December, meaning she died for months. The Ava they encountered is also a Replicator. They come to the Stanton Research labs, where Ava has disappeared, with a note saying “I never meant for any of this to happen. I am very sorry. Ava”. They then discover that Ava is a different type of Replicator, one programmed with social interaction skills and emotions. Sheppard then gets a message, saying that Nancy is waiting for him. He returns to Washington, and meets up with Nancy, she hands John a memory stick with everything she has found on Project Archetype. She also took the liberty in researching Sheppard, but realises this was a mistake. She then wishes him luck, says goodbye and leaves.

Now with the new-found information, Lee is able to find out a warehouse in Redding with “pre-assembled masonry panels”, which is actually a code word for shipments of Neutronium, the base material for Replicator nanites, so the Replicator could go there to repair. Bates organises a stake-out, in case the Replicator shows. However, they need a way to terminate it, but Sheppard gets an idea when Lee mentions a volcano, or molten steel, like in the movies.

The teams arrive in the warehouse at night, but couldn’t find the Replicator anywhere. However, it is inside the building, and knocks out the entire team, besides Ronon and Sheppard, where they attempt to fight it. However, the Replicator is about to kill Sheppard, where Ava saves him, and fights the Replicator in hand-to-hand combat. Unfortunately, the male model gets the upper hand throws Ava aside to deal with Ronon. Sheppard is then able to get a knife out and stabs the Replicator with it. The knife has a locator beacon and on Sheppard’s command, the Replicator is beamed away. Ava wonders where it it. Sheppard explains that he has sent it to low-Earth orbit. The Replicator is quickly destroyed through the friction of re-entry.

With the situation resolved, the team discuss what is to become of Ava. Despite the fact that she saved them, she is still too much of a security threat. In the end, Sheppard meets with Ava, and tells her that she can be free to roam around Earth, just as long as she is not to work in any scientific fields. Sheppard wishes her luck, and she walks. However, Sheppard then inexplicably disappears. It is revealed that her consciousness has been transferred into Virtual reality, giving her room enough to explore her own World, without her knowing. They also destroyed her body.

In the end, Ronon plans to go back to Atlantis. However, Sheppard decides to stay a little longer. He takes a taxi to a house, where his estranged brother, Dave lives. He enters the house, where they have a discussion.

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Lieutenant Colonel John Sheppard and Doctor Rodney McKay meet with Flora and Mardola, the royalty on a planet the Atlantis Expedition trade with since their first year of operation, where they also warned them of a Wraith culling.

The two sisters are very grateful for their kindness and toasts them for it. The sisters then says they need the mens help, they have another sister that needs their assistance. When they step out for a second, the team are expecting a sister as beautiful as Flora and Mardola, but they are stunned, when they are met by the third sister, who is actually thirteen years old, named Harmony.

Flora and Mardola explain that their mother, who was Queen, recently passed away. They performed a ceremony, and later determined that Harmony is to become the next Queen. There is a rite of passage Harmony must go on to the Ruins of Larris, to become Queen. Originally, the next of kin would travel alone, but since Harmony is 13, the other sisters fear for her safety. They explain that although the planet’s residents are prohibited from escorting the new queen, the law does not apply to visitors from other worlds. They appeal to Sheppard and McKay based on maintaining their alliance, and they reluctantly agree.

McKay and Sheppard take Harmony into the woods, and she finds out that Sheppard is the leader, despite Mckay’s attempts to argue against it. She wonders why Sheppard puts up with Rodney’s impertinence. On the way, Sheppard follows the map, when he notices that a wooden bridge over a ravine has since collapsed, and sees no other way to cross. He tells McKay to stay with Harmony, while he looks for another way over. While he is gone, Harmony takes a power bar from his pack, against McKay’s wishes, and she opens it. When McKay tells her to take it back, she hands him the empty wrapper. When Sheppard returns, he thinks McKay took his food, despite him saying Harmony took it. McKay then aggressively tells Harmony to tell the truth, when she bursts into fake tears. The deceived Sheppard takes pity on her, who agrees on letting her navigate using the map when they return to the path.

After more navigating, they all hear a strange noise. Harmony tells them that it is the sound of the “beast”, which is assigned to attack anybody, or anything that is a threat to the throne. After some further walking, McKay and Harmony notices that Sheppard has disappeared. Harmony wonders why McKay isn’t taken, since she thinks the beast is behind this. This is proven to be wrong, when McKay is surrounded by a group of three Genii, who don’t seem to recognize him, since he helped them with their nuclear weapons program. They tell him that all they need is Harmony, and they’ll spare him. McKay considers it for a second, but then Sheppard (who had sensed the ambush,) shoots them all down from behind the foliage.

They wonder what the Genii are doing here. Harmony reveals that her people used to trade with the Genii, but after they kept cheating them several times, her mother banished them. Sheppard leaves McKay with Harmony again, to find out how many more Genii are out there. During that time, McKay and Harmony continue their arguments, whilst Harmony tries to intimidate Mckay with threats, for fun. Sheppard returns to them, and tells them that there are Genii everywhere. They decide to hide out until nightfall, where they would then return back to village. However, Harmony disagrees, since she wants to make it to the ruins before the end of the lunar cycle. The known her throne will be forfeit if she fails the quest. Sheppard however, has to insist on returning, since it isn’t safe to continue.

In the palace at night, the Genii leader, Toran sneaks into the palace, and meets up with Mardola, one of Harmony’s sisters. They both have a secret meeting. It is revealed that Mardola has ordered the hit on Harmony, and would become Queen herself if she were not to return from the ruins. Toran blames her for the death of three of his men. But Mardola simply states that having Sheppard and McKay around was unfortunate, and agrees on paying the Genii three times as much as she originally intended to give them. Toran gives her a radio to contact him. She also tells Toran to keep the fact that she ordered the hit on Harmony a secret, as if anyone finds out, it would be bad for both of them.

Meanwhile, McKay comes up to Sheppard, and suggests that they stun Harmony and take her back. Sheppard disagrees, and decide now would be the time to head back, whilst it is still dark. However as they turn around to tell Harmony, they notice she has disappeared. They proceed to search for her in the woods, but can’t find her. McKay then feels hungry, when Sheppard admits that having Ronon there to track her down would useful. Rodney smells a fire and food and is able to track the origin of the fire.

They find Harmony hidden in a cave, and sees that she has caught a Loden bird and started a fire to cook it. Sheppard quickly puts out the fire, and warns Harmony that she is in trouble. They have to turn back to the settlement, despite Harmony telling them that the ruins aren’t that far away. As they plan to leave again, they hear the beast approaching. They decide to wait it out and then turn back. Later they chat and Harmony says that since she is going to be Queen, she is going to need a King, and suggests that Sheppard become her king. However, he defers. They then hear the beast again and screams and weapons fire coming from the Genii. Sheppard goes to investigate, and again leaves McKay with Harmony. Harmony wants McKay to teach her about love, since she thinks that she’s in love with John. McKay advises her that Sheppard won’t be interested in her, and she would have to find her own King. Mckay realizes she was only having fun back in the forest and that she is not really so bad, admitting he “doesn’t not like her.”

Meanwhile, Sheppard finds two Genii bodies, who have been attacked violently by the beast, and turned into “Swiss cheese”. He then hides from other Genii soldiers, who find their dead comrades. When they leave, Sheppard discovers that the Genii now have a shoot-to-kill order on the three of them. When he overhears the communication, Sheppard returns back to the cave to go back. Harmony disagrees, since they’re close to the ruins, and insists the beast will avoid the ruins. Sheppard finally agrees and decide to leave as soon as possible.

As dawn sets, the trio arrive near the nearby ruins and takes cover, where they find two Genii soldiers fiddling with some Control crystals on the ruins. McKay gets his stunner out and begins to aim, but Sheppard quickly snatches the weapon off him and does it himself. When they arrive in the ruins, they notice that the structure is Lantean architecture. McKay discovers that the “ruins” is actually a testing place Mini-drones. McKay explains that the noise of the beast, is just the noise of the drone’s engines. Also, the drones haven’t attacked the trio, because they all have the ATA gene. Unfortunately, the Genii have fiddled with the control crystals, meaning the drone controls wont activate. Harmony gets out her pendant to control the “beast” and explains it will light up once she activates the neural interface but Mckay realizes that because of the tampering from the Genni, the controls will not function. Harmony sees her pendant not glowing as a sign that she should not be queen. Sheppard tries to explain that it’s just broken and that Mckay can fix it.

Whilst McKay replaces the crystals in the correct order, Harmony insists she can make it work if she focuses (believing that the Lantean technology is holy and cannot be destroyed,) but after several tries begins to believe she is not the true queen after all. Toran then radios the Genii prisoners, and Sheppard tries to bluff through a conversation that he is Heiron and everything is fine. However, as the two Genii cry for help. Sheppard stuns them again, as Toran announces that back up is on its way. Preparing a Genii attack, Sheppard takes cover with Harmony, while McKay works on re-activating the device. However, just as he is completed and the device powers up, the Genii starts firing on them.

In the process, Harmony runs towards cover. He runs to her and trips whilst trying to push her out of the way, dropping her to the ground too. They get up and run to Sheppard’s cover spot. Toran admits that one of her sisters ordered the hit, when she says her sisters would take them down. McKay isn’t sure if the device is working. Sheppard then plans to activate the device. He tells McKay to lay down cover fire, while he snatches Harmony’s pendant, since anyone with the Ancient gene can activate the drone system. He makes a run for the device and commands the drones with his mind, and the drones mobilize and kill Toran, as the others run away and the drones chase them. Harmony is duly impressed by McKay, and declares him a hero, because he shielded her from the Genii with his own body, to which McKay responds he just fell. She also starts to denounce Sheppard for taking her pendant. She then places her pendant over the device, making it glow, and is pleased to know she is the true Queen after all.

They return to the palace and search Mardola’s quarters, since they searched Flora’s quarters and found nothing. They find the Genni radio. Mardola explains that Harmony is too young to become Queen, to which Harmony says that by the time she will be released from jail, she will be too old to remember it, and has her arrested. McKay and Sheppard later attend the coronation, where Harmony congratulates McKay and Sheppard for their work in protect her. She then unveils a portrait of the event painted by her best artists. The painting shows a heroic Harmony in the middle, with brave McKay defending her from the Genii and Sheppard cowering in fear behind her.

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It is a normal day in the city of Atlantis, with Expedition members performing their usual duties. In the lab, Lieutenant Colonel John Sheppard plans to play a computer game of golf with Doctor Rodney McKay.

However, he plans to have lunch with Katie Brown, but with a surprise. He brought a diamond ring from Earth, and plans to marry Brown, since they saw each other for around two years. Sheppard promises to get him a beer after this to congratulate. McKay then leaves and in the way, passes Teyla Emmagan, now visibly pregnant, who comes to see Sheppard. Meanwhile, Doctor Jennifer Keller sees Ronon Dex, who has, yet again injured himself in a sparring session. Also, Colonel Samantha Carter joins Doctor Radek Zelenka in the transporter to the main tower. McKay joins Brown in the botany lab to get some lunch. A nervous McKay then reaches down to get the ring. However, as he is about to, an alarm sounds and the door behind them closes. He is not the only one, the entire city has mysteriously locked down.

Sheppard, Keller and Carter separately calls McKay for help in what is going on, but there are no answers. Zelenka notices that communications are down. Meanwhile, McKay explains to Brown that they are in a quarantine lockdown. He tweaked the system after the Kirsen fever, since the quarantine had not took affect then. Now that he knows what is going on, he needs access to a computer to stop it. However, Brown says he can’t since she left the computer and radio in another room, that can’t be reached because of the lockdown. In the infirmary, Keller has Ronon help her ready the infirmary, since she knows that this is also a quarantine.

John and Teyla discover that they are in a “category five” lockdown, the highest level, meaning absolutely everything is out; ventilation, communications, long-range sensors, as well as all primary and secondary systems. Teyla then tells John that she originally came to discuss the future of her position in the team, due to the child. If the rest of the Athosians aren’t found, then she may have to pull back, since she doesn’t want her son to grow up without a mother. Sheppard then assures her that if something does happen, then Atlantis would be the son’s family. Meanwhile, Carter and Zelenka, who are also trapped figure out the quarantine status. Carter starts to doubt if there is a disease outbreak, since everything is down. Their suspicions turn out to be correct, last night, there was an intense ionospheric storm, which spiked Atlantis’ power, causing it. Now that they know what is behind it, they wonder why McKay hasn’t figured out the problem yet, not knowing he has no access to a computer.

In the botany lab, the couple get into an argument on what to do next. Afterwards, McKay decides to cheer her up, but couldn’t think of anything, until he notices the Rodneyana villosa, which has fully grown. McKay then starts to feel ill, believing the disease as got him, not knowing there is no outbreak, and is likely just allergic to some of the shrubbery and plants.

Ronon, who doesn’t like sitting around decides to force the door open, tearing up his stitches in the process, but the door still won’t budge. Keller frustratingly restitches his wound. They decide to both talk to pass the time. However, they can’t find anything to speak to him about. Soon, Keller starts to admit that she is not good at sitting and waiting either, since nothing has happened for a while. Ronon starts to talk about how she reminds him of Milena, his former lover who was killed on Sateda during a Wraith attack several years ago, trying to save her people. Keller tells him that there was nothing he could’ve done to make her come with him, if she wanted to stay and help her people.

Meanwhile, Sheppard feels unnerved that “in the movies”, the pregnant woman always gets into labour, despite Teyla saying that the baby is months away. Sheppard then plans to hack into McKay’s systems, and does so by typing his password, which Rodney once told him, because he never thought John would remember it. He types McKay’s password, which happens to be 16431879196842 (a combination of Isaac Newton, Albert Einstein and McKay’s birth years, and 42, the ultimate answer to life, the universe and everything). There, he discovers that the city has activated a distress signal since the lockdown, which is leaving their position vulnerable. He still can’t go to the control room. Teyla’s baby then starts kicking. Sheppard plans to blow the door open, but can’t find any explosives. With no other option, Sheppard breaks open a window, and plans to climb up to the control room, which is only four levels up. He starts to climb up the central tower.

Carter and Zelenka are starting to get a little hot, since the ventilation is down, no cool air is coming. They plan to use the computer to get the transporter door open. However, in the process, a power surge knocks Radek back. The surge also burnt out the RAM, meaning they are now stuck for good. Sheppard continues to climb up Atlantis, and almost falls on one occasion. However, he is able to make it up to the control room balcony and then breaks himself into the control room. There they find a group of technicians frantically working on restoring the ventilation, which they restored on the central tower, and tries to stop the distress call, which is protected by McKay’s password. Sheppard is able to get into McKay’s system and shuts down the signal. However, there is another problem, since Sheppard broke into the control room, this means that there is a breach in quarantine, which causes all the computers to shut down and the self destruct sequence activates.

After hearing the destruct sequence, Ronon tries to open the door again, without any success. Since he doesn’t have his weapon with him to blow the door open, he plans to find explosives, despite the fact that it is an infirmary, not armoury. He then has an idea when Keller mentions the oxygen tanks. He plans to use an oxygen tank and shoot it to blow a hole into the door, similar to how Sheriff Brody stopped the shark in the movie “Jaws”. However, since there are no guns in the infirmary, he uses Keller to score some marks into the neck of the tank. Meanwhile, Chuck is able to shut down the alarm, but not the self destruct sequence. The only way to stop it, is to go down six levels, enter the Power room and shut down everything to reboot the systems. With half a dozen doors to get through, they plan to blow through them. However, Major Evan Lorne only has one block of C-4. A team of Lorne, Sheppard, Chuck, and Amelia Banks starts to climb down Atlantis.

McKay is now lying on the ground in the botany lab, and tells Brown that the technicians may have only muted the alarm. There, Brown notices the ring McKay is carrying, and McKay admits that he came to her today to propose to her, but now that he thinks he is dying, says there is not much point in doing so, which upsets Brown a little. In the infirmary, Keller is done marking the oxygen tank. Ronon sets up a contraption, by using a few hospital beds, a scanner and another oxygen tank. From a distance, the two take cover behind a wall, where Ronon then activates the scanner, where the second tank falls onto the end of the other tank, where it acts as a missile, and then bounces off the door, before flying past Keller and Ronon. When they check if the door opened or not, all they saw was the a lot of mess, and the door hasn’t opened.

Sheppard and the team are now inside the city, and uses the last of their C-4 to blow a door open. There, Carter and Zelenka hears the noise and shout for help. Sheppard hears them, and he and Lorne help open the transporter door, since they aren’t as strong as the other doors. There, the two are briefed on the situation. With no more C-4, they see an air vent, which leads to the power room. Zelenka volunteers, since he is small enough to fit. The team helps him up, and he crawls though the vents.

In the botany lab, McKay is still lying on the floor, with Brown not talking. In the infirmary, Ronon admits to Keller that when she first arrived, he thought she was weak, but has a change of heart since the attempt on scoring the oxygen tank. Keller tells Ronon that there was never a part in her life where she belonged, since she was focused on education more than her personal life when she was younger.
Zelenka falls into the power room, stands up and limps to the control switches and turns them all off. Ronon ad Keller are about to kiss, when the power shuts down. When it reboots, the entire city has now become fully operational again, with the lockdown overwritten, and the self destruct sequence deactivates. This distracts Keller and Ronon from their very near kiss. Meanwhile, McKay is relieved that the doors opened again, but looks awkwardly at Brown, who is holding the ring.

In the mess hall, the whole team congratulates Radek on his work in shutting down the lockdown, and all owe him a debt of gratitude. Carter also informs them that for 24 hours now, there has been no sign of any ships, Wraith, or otherwise that has detected the signal, and are all in the clear. Ronon tells them that he heard McKay thought there was an actually quarantine, since he was sick, but stops talking when Keller arrives. Sheppard and Teyla then tease Ronon about a possible relationship between him and Keller.

Meanwhile, McKay returns to Katie in the botany lab and admits that after the lock down experience, he has realized that he has “shortcomings”, like McKay, and says he isn’t ready for marriage and doesn’t want to risk ruining her life until he’s worked out his own personal problems. Katie also admits that she’s not quite ready for marriage either, and both she and McKay agree to put off the proposal for a future date, and having a raincheck on lunch. As Rodney heads to the door, Katie said “bye” with a very sad look on her face, before the door closes.

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