While walking through the halls of Atlantis, Dr. Weir is approached by her new acting head of medicine, Dr. Jennifer Keller. Dr. Keller is daunted by the task of managing the entire medical staff for the Atlantis Expedition in the wake of Dr. Beckett’s death (ATL: “Sunday”), and asks Weir to replace her as soon as possible. Weir says that’s up to the IOA, but for right now, she tells Keller that dealing with the pressure will get easier over time; she should get used to her new position.

As Weir enters the control room, Dr. McKay approaches her and complains about having to fill out personnel evaluation reports for the people under his command. When she tries to convince him that it is necessary, Col. Sheppard enters the room, turning in his already completed reports to Weir. She is annoyed when she sees that he has ranked everyone with “excellent” and “above average”. He retorts that they did perform excellently and above average, and a good leader shouldn’t lie. Before Dr. Weir has a chance to respond, they are notified that Earth’s newest Daedalus-class battlecruiser, the Apollo, has just dropped out of hyperspace. The commander, Colonel Abe Ellis beams down to the city and meets with Dr. Weir and her staff. He has come to inform them that the Daedalus, which has been conducting routine reconnaissance of the Asuran homeworld, has detected evidence that the Asurans are building a fleet of warships with the possible intentions of attacking Atlantis or, even worse, Earth. Ellis informs Weir and her senior staff that he will be conducting a preemptive strike against the Asurans to see that they never have an opportunity to launch their ships.

After viewing images taken by the Daedalus evidencing the construction of the ships, the IOA authorized this first strike. They sent the Apollo to Atlantis with the Horizon weapons platform on board. Horizon is a module containing six Mark IX “Gatebuster” nukes and four decoys that can be deployed from orbit. While Dr. McKay argues that since the Asurans are actually Replicators, if just one nanite survives, they will be able to reproduce their society, and Horizon doesn’t have the power to destroy them all. Col. Ellis explains that their target is only the new Asuran ships; they are constructed of conventional alloys, so the Mark IX’s will be enough to completely eliminate them. Once the scientists at Area 51 complete their latest project, the Planet Wide Anti-Replicator Weapon, or P.W.A.R.W., Ellis and the Apollo will return to the planet to destroy the Asurans for good. For now, though, this will have to do.

McKay and Zelenka beam up to the ship to inspect the Horizon and prepare it for launch. Meanwhile, Weir expresses doubt about the whole idea; the Asurans haven’t recently made any aggressive moves against Atlantis. Attacking them now would invite a counter-attack upon the city that could have disastrous effects. Col. Ellis proceeds anyway, despite her warnings. Upon arriving in orbit of Asuras, Ellis deploys the Horizon, which successfully delivers the nukes through the atmosphere to their targets. The mission is a success, and the Asuran ships are obliterated.

Later, an object is detected exiting hyperspace and entering orbit of Lantea. It’s not a Wraith ship, but it doesn’t have a recognizable transponder signal either. Apollo moves in range to investigate, and finds that it is a small satellite with a stargate inside it. As the ship moves in closer, the Stargate activates, and shortly thereafter, the satellite manoeuvres so that the wormhole’s event horizon faces the Apollo and fires a sustained energy beam at the ship. The ship’s energy shields are quickly drained. Before it is seriously damaged, though, the satellite rotates, moving the beam down to the planet, sweeping toward Atlantis. The city’s shield is raised just in time. The beam is sustained and fires continually at the city.

Dr. McKay briefs Atlantis’ senior staff and Col. Ellis about the attack on the city. The satellite is protected by a shield powered by the beam, and the beam itself is powered by a large number of ZPM’s; clearly, this is the work of the Asurans. With this near-infinite power source, the Asurans will be able to maintain the wormhole and the energy beam indefinitely. Unfortunately, the humans can’t maintain the city’s shield anywhere close to indefinitely; their sole ZPM will be depleted in 29 hours. Then, the shield will fail and the city will be destroyed.

Weir opens communications to Asuras through the satellite gate. She is surprised to see Oberoth again. He tells her that each Asuran exists within a collective consciousness and can be replicated multiple times. Her efforts at diplomacy fail, and when the Asurans try to send a computer virus into the Atlantis mainframe, she terminates their communication link.

In light of recent events, Sheppard goes to Col. Ellis and confronts him about the negative repercussions of their mission. Ellis responds that he is just speaking on Weir’s behalf. Ellis goes on to say that while John has blemishes on his record, he should be the one leading Atlantis. Meanwhile, Teyla meets with Weir, and the expedition leader reveals that she is deeply troubled by the threat Colonel Ellis poses to her authority. She rants to Teyla that the IOA may back her regularly, but when Atlantis faces dangerous circumstances, Weir is nothing more than their scapegoat. Worse than the IOA, though, is the military; sometimes it seems like General O’Neill is the only one in the military who supports her command of Atlantis. She muses to Teyla that if they survive this, she may have to step down. Teyla tries to be reassuring but is clearly troubled by Weir’s words.

Later, while reviewing possible options, Dr. McKay and Dr. Zelenka reach a brilliant solution to their problem; submerge Atlantis to the ocean floor. The Ancients did it once before, ten thousand years ago. Previously, the team couldn’t submerge the city because several necessary systems were offline. However, those systems were restored when the Ancients returned to Atlantis (ATL: “The Return, Part 1″). Once underwater, the beam’s intensity will be attenuated. Its weakened strength will buy Atlantis more shield time. This is by no means a permanent solution to the problem, but it will buy them several hours to come up with one. Weir gives the go-ahead, and McKay makes the necessary preparations. The city sinks and lands on the Lantean ocean floor. Sadly, McKay and Zelenka find that the three hours of work necessary to sink the city have saved the ZPM only nine hours worth of shield power. Another solution must be found very quickly.

Col. Sheppard and Dr. McKay realize that they will always be in range of the satellite on Lantea, and their only hope of escaping the beam is to leave the planet and escape to space using the city’s stardrive. The problem is, there’s not enough energy in the ZPM to lift the city out of the atmosphere while shielding it from the beam at the same time. In another shared stroke of genius, McKay and Sheppard suggest to Col. Ellis that he dispatch Major Lorne to lead a squadron of F-302’s toward Lantea’s moon. The squadron will tether themselves to one of several asteroids orbiting the moon, and maneuver it into the beam. If all goes according to plan, it will disrupt the beam for several crucial minutes during which the shield’s stresses will be alleviated. Even then, one ZPM wouldn’t be enough to operate the stardrive, but supplementing it with power from the Ancient geothermal drilling platform (ATL: “Submersion”), it should be enough to get into the atmosphere.

The plan is approved. All non-essential personnel are evacuated to the Apollo, and the F-302’s make their way to the selected asteroid. Col. Ellis tells Weir that while he may not like her, he does respect her, and he apologizes for attempting to overstep his authority. Weir appreciates the gesture; Ellis returns to his ship, the F-302’s move the asteroid into the beam’s path, the geothermal platform works perfectly, and the city begins its ascent.

Unfortunately, there is still not enough energy to power the stardrive. The city makes it to the ocean surface but can’t get far up into the atmosphere. Weir suggests dropping the shield; McKay argues they won’t be able to contain an atmosphere without the shield. However, Sheppard, flying the ship from the control chair, agrees that they should deactivate it; they won’t need artificial atmoe satellite’s beam hits Atlantissphere until about 18,000 feet. Once the shield is down, Atlantis moves off into the atmosphere. After reaching 18,000 ft, Sheppard engages the shield. However, at that moment, the Asuran beam destroys the asteroid blocking it, and races down toward Atlantis. It strikes the city before the shield closes, grazing the control tower. Several windows blow out, and the blast from the beam injures many people, including Ronon and Weir. The control room is severely damaged. Despite the damage, Sheppard gets the city out of harm’s way, exiting the atmosphere and going into hyperspace. He then receives word from McKay that the control tower has been hit.

Minutes later, Sheppard arrives at the control room. There is heavy damage and many injuries. Dr. Keller loads Weir onto a stretcher. She appears to be severely injured. When Sheppard tells her she’ll be okay, Keller says she isn’t so sure about it. Sheppard goes into the control room, and finds Ronon there, severely injured, having to order him to get medical attention. Immediately after, Atlantis abruptly drops out of hyperspace. McKay realizes that they have not arrived at the planet designated to be Atlantis’ new home, M12-578. Rather, they are truly in the middle of nowhere; there are no nearby stars, planets, or other navigational markers. Atlantis is lost in space, and neither McKay nor Zelenka know what happened to the hyperdrive. Worse, the ZPM has 24 hours of charge left. When it has expired, they will lose atmosphere and die.

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Dr. Weir reports that the Taranians haven’t contacted Atlantis in over two months. John Sheppard’s team is sent to look for them. On the Taranian settlement they discover it appears as though the whole settlement has been abandoned.

Detecting a life sign below them, the team searches an underground complex made by the people who lived there before the Taranians. There they are faced with a large creature which has similarities with the Iratus bug, after finding a room full of dead Taranians, an Iratus Bug in a jar full of liquid and a large cocoon/pod in an empty room.

After a scheduled check in, and before the team comes into contact with the life sign, Dr. Weir sends them a Marine contingent to help them deal with the creature, but soon after they arrive they are abducted by a Wraith dart.

After Sheppard’s team has little luck with destroying the creature (Ronon only manages to cut off its arm) and realizes they’ve lost contact with the Marines, they try to return to Atlantis, only to find that the control crystals have been removed from the DHD, disabling the gate. Returning to the complex they discover that Michael Kenmore, after being rejected by the Wraith began experimenting with the bug and created these creatures to take over the galaxy. They soon discover that he has hundreds of those creatures on that planet and this is not the only planet on which he is breeding them.

While McKay and Teyla stay in Michael’s lab, McKay tries to figure out what Michael was doing and how many creatures are on the planet. Meanwhile, Sheppard and Ronon use the air vents to get to the surface and locate the control crystals. Unable to find the control crystals and with the creatures on their tail, they quickly find Michael’s Wraith dart. Sheppard is able to fly it and then beam Ronan, Teyla, and McKay on it and then use its DHD to dial out.

Daedalus is redirected to go and nuke the planet but when they arrive there they find that the whole place is wiped clean with no sign of Michael or the creatures.

At the very end of the episode, Dr. Weir explains to Teyla that it was their fault the Taranians were killed, as the Wraith discovered their location after they hacked the Atlantis Database during the episode Allies. Dr. Weir also mentions that according to what McKay was able to decipher from Michael’s device, there are at least three other planets where Michael was conducting his experiment and there are hundreds of beasts out there.

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In the water beneath Atlantis, a large contingent of Atlantis personnel are aboard a Puddle Jumper searching for a mobile drilling platform on the ocean floor, including Dr. McKay, Dr. Weir, Dr. Zelenka, Teyla, Ronon, and Colonel Sheppard. Zelenka and Ronon are complaining that the search is taking too long. McKay starts to argue with both when a Doctor Graydon supports McKay, crediting McKay with narrowing the search field to a remarkably small area. McKay appreciates the comment and welcomes the new Dr. Graydon to the team, only to find out that he has been at Atlantis for over eight months and is not the Dr. Grayson that McKay originally wanted to join the team.

After hours of searching, they finally find the station and begin docking procedures which in turn powers up the station. The camera switches to a close up of a set of Wraith eyes opening.

Aboard the station McKay reports to Weir that the station systems are all online and functioning at full capacity. Weir cautions McKay to slow down before producing energy from the station, until they find out why the Ancients abandoned it. Ronon, Teyla and Sheppard are exploring the station when they realize they are going in circles. Teyla then realizes she senses a Wraith presence within the station. Everyone retreats to the station’s control room.

McKay, in spite of protesting, runs a life sign scan on the station and finds nothing out of the ordinary. Weir reminds the team that Wraiths can not be seen on life scans if they are hibernating. Ronon asks if Teyla’s senses have ever been wrong, and she replies that they haven’t.

Despite the scans, Teyla offers to reach out with her mind to find the Wraith. Weir, Ronon, and Sheppard all watch Teyla reach out with her mind, in order to prevent her from causing trouble, similar to earlier episodes where Teyla was taken over by a Wraith when she opened her mind too much. Teyla awakens from her trance dazed but says she was unable to find anything, and blames the water pressure. Sheppard is glad he will not relive the movie The Abyss. Weir and Sheppard split from Ronon and Teyla in order to explore the station more.

While searching, Teyla is being very quiet, which concerns Ronon, and he confronts her. Teyla apologizes and places her hand on his shoulder explaining that he is a good friend, and that she would not want to do anything that made him uncomfortable. Suddenly Teyla viciously attacks Ronon, knocking him out and leaving him behind. She walks in a trance to an auxiliary control room and begins powering down sections of the station.

Weir and Sheppard are in one of the blacked out sections, prompting them to call into McKay who still has power but finds out 40% of the station has been powered down. McKay explains that the station has been on the sea floor for a few millennia and could have blown a fuse. Sheppard tries to contact Teyla and Ronon but Ronon is still unconscious and Teyla is not responding. Sheppard asks McKay to see if he can find either of them, but he replies that the internal sensors are down. He reports the power outage was attributed to a control room in the search area that Teyla and Ronon were exploring. Sheppard and Weir go to find out what happened. McKay sends Dr. Dickinson and Dr. Graydon back to the use the jumper sensors in order to find Ronon and Teyla.

McKay, Sheppard and Weir all meet up and begin looking for Teyla and Ronon. Teyla opens a control panel exposing some of the control crystals. She then pulls her sidearm and proceeds to destroy the crystals. McKay, Sheppard and Weir hear the shots and run to follow them.

In the lower levels of the station the Wraith comes into the station via an open water access door in the floor of the station.

Sheppard, Weir and McKay find Ronon, and discover that Teyla attacked him. Teyla continues working at the control panel initiating emergency force fields around the station. Weir and McKay make their way back to the control room while Ronon and Sheppard go to find Teyla. Teyla awakens from her trance and stares at her empty gun, and then is discovered by Ronon and Sheppard with no memory of what occurred for the last hour.

McKay finds out that Teyla not only powered down sections of the station she scrambled the operating system code, and disabled the communications center. Weir meets Teyla, in the crew quarters with Sheppard and Ronon. Teyla apologizes and explains what happened. When she opened her mind she found out the Wraith was a Queen. She found the Queen’s mind to be very powerful but then remembers nothing else until Sheppard and Ronon found her. Ronon and Sheppard go to look for the wraith and Teyla offers to help but Weir is wary of Teyla doing anything until she is certain the Queen is not still controlling her.

Dickinson and Graydon are working by themselves in order to disable the force fields. A force field cutting them off from the jumper is disabled, but both are unsure if it was due to what they were doing. Dickinson sends Graydon to check it out. Graydon finds wet footprints from the force field to the jumper. Graydon is inspecting the jumper when the Wraith Queen attacks Graydon from within the jumper.

Back in the control room McKay and Zelenka are debating why the Wraith would be on the station. McKay sends Dr. Coleman to reprogram the station’s external sensors to see if there is anything of note in the area.

In the crew quarters Teyla and Weir are discussing the Wraith Queen. Teyla feels embarrassed for harming Ronon but Weir thanks her for using her power to discover the Wraith. Teyla tells Weir that the Queen was only able to control her because she had her mind open and was not ready for her. A mistake she will not make again.

Ronon and Sheppard are still searching for the Wraith when they hear Dickinson being attacked by the Wraith Queen. Both run to help Dickinson but are cut off by the emergency force fields. McKay and Zelenka finally disable the force fields. Sheppard makes it to the Jumper and finds Graydon after being fed upon. Sheppard whirls around to find the Wraith Queen, who forcibly controls his mind so that he can fly her back to the Stargate, so she can return to her people. Ronon jumps out from behind the Wraith and fires a shot, but using Sheppard who can see Ronon, the wraith jumps out of the way and the shot destroys the jumper’s window that is exposed to the outside of the station, letting in sea water and knocking all unconscious.

Sheppard and Ronon wake up to find themselves in the hallway due to the force of the water. McKay initiated the force fields to keep the water from flooding the station, effectively cutting everyone off from the jumper. Ronon and Sheppard look around and discover the Wraith Queen is nearby and still unconscious. They decide to capture her rather than kill her since she may know a way out. However, the Queen refuses to tell them anything, other than that they are about to die.

In a rare moment of humility, McKay is arguing with Zelenka that he should have trusted Teyla. Zelenka offers the repeated life scans that did not show anyone else on board. Coleman comes back and offers that the Wraith came on board after the scans. The external sensors have revealed a Wraith cruiser almost buried in silt about a kilometer away. The crew sumarises that the Queen swam from the cruiser to the station.

After restraining the Queen, Teyla tries to enter the Queen’s mind to find out how the Wraith came on board and if there is any more Wraith around, and why she keeps saying they are all about to die. The Queen says Teyla is too weak, but Teyla digs into the Queen’s mind. She finds out that the Queen was in the first wave of ships that attacked Atlantis, Queen of a great alliance. Her ship was damaged and crashed into the ocean. She fed off of her crew for centuries and was awakened from her hibernation when she sensed Teyla nearby. She left her ship and made it to the station so she could make it to freedom. She made it to the jumper but did not possess the ancient gene to fly it, and needed Sheppard. Teyla then finds out that the Queen set the auto-destruct sequence on the Cruiser before she left it, and it will detonate in two hours.

McKay makes the startling discovery that the planet’s crust is very thin where they are located and there is a large energy potential there. The explosion of the Wraith Cruiser will be magnified by the large amount of magma nearby and will also wipe out Atlantis. Everyone is unsure about what to do. The self destruct needs to be deactivated, but the jumper is disabled and there is no other way to get to the ship, until McKay remembers seeing a type of deep water suit that was used to do maintenance on the station.

Sheppard and McKay walk to the remarkably intact Wraith Cruiser and get to the main control panel with 30 minutes to spare but find out that they need an access code to disable the self destruct sequence. The Queen refuses to reveal the code prompting Teyla to try to entering the Queen’s mind to acquire it. She loses her control momentarily and Weir stops her from trying again, fearing she is too weak.

Teyla tries to convince Weir that she can get the codes, but Weir is unconvinced and tells her no. Weir heads up to the control room and Teyla sends Ronon up to help her leaving her alone with the Queen. Teyla tries to enter her mind again but is quickly overcome by the Queen, and she begins loosening the Queen’s restraints. The newly freed Queen jumps at Teyla but discovers that Teyla is trying to hide something in her mind. The Queen digs into her mind and discovers a conversation between Teyla, Sheppard and Weir. They discuss the Wraith Cruiser and how that it is still flyable but that they still can not deactivate the destruction codes. The Queen knocks out Teyla and swims to the Cruiser.

The Queen surprises Sheppard, deactivates the self-destruct, and tells him that she is going to “reward” him for fixing the engines, “with a quick death” Suddenly McKay jumps out from behind her and opens up with his P90 submachine gun, but even unloading the entire magazine doesn’t kill her. The Queen whirls around only to be shot more in the back by Sheppard’s sidearm. Teyla actually planted the memory of the meeting for the Queen to find so that she would escape and deactivate the self destruct sequence so she could escape in the Cruiser.

Everyone is in the crew quarters when McKay reports that everything is operational again and is excited to continue exploring the station. Weir and McKay go off to continue research of the station while Sheppard, Ronon and Teyla all go to bed to recover.

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On an extraordinary day in the city of Atlantis, it is the mandatory rest day, a type of day sanctioned by Dr. Kate Heightmeyer to give the Atlantis Expedition some time for recreation. Teyla Emmagan is talking with Dr. Hewston, who just finished a sparring session together. They both notice that so many people are having some time off. They also discuss a man who took a fondness for Teyla, though she didn’t want to discuss it further, stating the ways of her people are different. After the discussion, they both agree to have a late lunch together.

However, just as they enter the mess hall, Teyla remembers that she left her bantos sticks behind in the gym. Just as she turns around to fetch her things, there is a massive explosion behind her and she gets thrown across the corridor. She realizes that a bomb has just gone off in the mess hall. As she attempts to get up to help the wounded, she stops, due to shrapnel being lodged in her abdomen.

Three hours before the incident, Dr. Elizabeth Weir is in her office catching up on some work rather than relaxing, when a handsome young scientist, Mike Branton finds her. He wonders why she is working on her day off, as she has ordered everyone else to do. It also turns out, Branton is catching up on work, but has just finished. He invites her to lunch, but she thinks that it is a date, since she has a personal rule not to be involved with people under her. However, Branton insists that it is not a date, just friends or co-workers going out for lunch. He eventually persuades her to come. She agrees to go with him in one hour.

During that time, she passes Dr. Beckett, who was planning to go fishing with McKay on the mainland. He notices that she is hiding something, and just guesses that she is going on a “hot date”, but agrees not to tell anyone. Weir later makes it to Teyla’s quarters. Initially, she was to have lunch with Teyla, but she had other arrangements, she agreed to go sparring with Hewston. Weir then decides to join Branton for lunch.

During their “not a date” lunch, they argue about whether a man and a woman can be just friends. He later decides to take Weir to the outskirts of the city to enjoy the view of the ocean. Weir then finishes her bottle of water, meaning that lunch is over. Branton admits that he should have brought dessert to last longer. He then starts admitting that he likes her and begins to wear down her shields, and even kisses her. She seems attracted to him, but decides she can’t allow a potential romance to bloom.

She is later saved from the awkward situation when the control tower radios her that there has been an incident in the city. When she arrives, she is informed that there was an explosion in the mess hall, with three people dead and more injured. They believe the explosion may have been caused by a bomb.

Five hours before the incident, Lieutenant Colonel John Sheppard and Ronon Dex plan to play golf with Teyla. However, Teyla regrets that she is behind on paperwork (which is an excuse not to play golf). Sheppard lets her off. Ronon then tells him that he has to catch up on mission reports too. However, Sheppard calls his bluff and takes him to the golfing area, where they meet up with Dr. James Watson, who is also playing golf, and Beckett, who plans to take one of them fishing. However, they all decline. Watson comes up to Beckett, complaining of a headache. However, Beckett points him to Dr. Cole.

Later, Ronon becomes bored playing golf, and takes Sheppard to the gym, to play a “real sport”. The sport turns out to be an apparent Satedan training sport, of capturing the opponent’s flag. Every time a level is complete, the next level becomes harder, such as using one leg, and one arm. Ronon easily beats him on rounds one and two. Sheppard later plans to stop playing, where he takes Ronon to his quarters to drink beer and listen to some music. There, Sheppard wonders if he left anyone back on Sateda, whether a wife or a girlfriend. Ronon says “close enough”, referring to Milena. Ronon wonders if Sheppard was married. He says that he used to be. They then hear an explosion.

They rush to the mess hall, where they see Dr. Zelenka examining the wreckage. Luckily, there is no structural damage. However, he tells them that McKay is checking up on something, and informs them that a few eyewitnesses claimed to have seen Dr. Hewston mysteriously blow up.

Fourteen hours before the incident, Dr. Rodney McKay is in the Atlantis infirmary in the middle of the night. He is with Beckett, Hewston and Watson. The two young scientists accidentally activated a device emitting radiation, but deactivated it. McKay shouts at them, telling them to take extra care. He later thinks his is being too condescending, and decides to give the scientists a break, by giving them tomorrow off. However, he wasn’t aware that it is the mandatory rest day. He looks at Beckett, who is imitating the retraction of a fishing rod, meaning the fishing trip they planned a month ago is happening today.

The next morning, McKay sees Dr. Katie Brown in her botany lab. He wonders if he could have lunch with her today, because he thought the month within the planning of the fishing trip and doing it was enough time to think of something to get out of it. He plans to take lunch to her in the lab. When he arrives in the mess hall, he sees Weir talking with Branton. Beckett comes in, thinking he has brought lunch for both of them. McKay then makes an excuse that he promised Katie to have lunch with her, since they are seeing too little of each other. He promises to come fishing next week.

Back in the botany lab, the couple were talking about the events over a year ago, with the Laura Cadman incident. She told him that he was ignoring her ever since for a year, but actually made time to see her the past few months. Later, they both hear an explosion, and McKay runs to a lab.

He informs Sheppard, Ronon and Teyla that the device Hewston and Watson activated, was an Ancient device created as a weapon. It uses an unusual type of radiation to create an explosive tumor behind a person’s lung. After an unpredictable period of time, during which the tumor grows, it approaches critical mass and then unexpectedly detonates. With Hewston dead, the only other infected person, Watson, is still at large. They try contacting him, but he is already in the infirmary, about to be operated on by Beckett.

Two hours before the incident, Beckett plans to persuade someone else to go fishing with him. He tries Zelenka, who is too busy playing chess with another member. He is playing for trades, and is winning. Beckett then comes to Major Lorne. But he’s too busy painting the city skyline. He then goes to Dr. Biro, but discovers her erratic personality. He officially calls the fishing trip a bust. He goes to Cole, who has a migraine and dismisses her for some rest, while he catches up on paperwork.

A while later, he treats a young woman with a sprained ankle from playing volleyball, when he hears the explosion. He rushes to the mess hall and sees Teyla, who he promises to take care of. After he finishes on Teyla, he starts working on Watson, when he gets a call from McKay. He tells him the situation, and to leave Watson. However, Beckett evacuates the level, but stays behind with a nurse to operate and remove the tumor. He locks down the section, meaning teams can’t get in to stop him. They attempt to talk Beckett out of helping Watson, but he refuses and operates on him.

Half an hour later, he took out the tumor, and sends it to a box. He is called to stay in the infirmary while the disposal team moves into the infirmary. However, he takes the box and slowly moves through a corridor and meets them half way. When they meet, he gives the team the box. He then proceeds in turning around and starts his return to the OR, when it suddenly explodes, killing him and the others nearby.

Before the memorial service, after which Beckett’s remains will be sent home to Earth for burial, McKay expresses guilt that he did not go fishing with Beckett earlier, because then he would not have been killed. However, Ronon tells him that there was nothing he can do, and tells him “what’s done is done”. Beckett’s memorial service is held in the Atlantis gate room with all of the staff in attendance, and Dr. Weir gives his eulogy. After the service ends, Beckett’s casket is carried through the gate back to Earth by McKay, Sheppard, Zelenka, Lorne, Ronon and Cole as the pallbearers.

After their return from Earth, McKay is standing on one of Atlantis’ piers grieving over Beckett’s death and sees a vision of him. He explains that his family was amazing, and later tells Beckett that it is his fault, and should’ve just gone fishing with him. Beckett comforts Rodney and tells him that it’s not his fault that he died. McKay says that he’s only saying what he wants to hear, and Beckett tells him, “That’s what best friends do sometimes. And in this case it also happens to be true”. Rodney admits that Carson was the closest thing to a best friend he ever had. They then say a final goodbye before Beckett fades away.

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Lt. Colonel Sheppard’s team investigates a derelict, centuries-old space station on a distant moon. Inside they find the last remnants of a civilization frozen in stasis using reverse-engineered Wraith beaming technology. One thousand men, women, and children were put into stasis in an attempt to avoid extinction at the hands of their longtime enemy, the Wraith.

Herick is the first to awaken when Sheppard’s team restores power. Placed in stasis in his mid-thirties, Herick is the technician who created the stasis device for his people. Though he expects to find his wife and son there with him, they are missing, along with the shuttle they were meant to arrive on. Angry, Herick awakens their leader, Jamus.

Due to riots following the launch of the first shuttle, Jamus explains, the second shuttle (with Herick’s family aboard) was left behind in order to conceal the existence of the sanctuary space station. Herick, distraught, commits suicide rather than live without his loved ones: He activates the shuttle’s engines and destroys the hangar bay doors, allowing the vacuum to suck him into space. This, however, also alters the moon’s orbit; it is now falling toward the planet with an exponential acceleration. As the Puddle Jumper has been pulled into space when Herick decompressed the hangar bay, both Sheppard’s team and the last remnants of the dying civilization are now trapped on board, doomed to die.

Dr. Elizabeth Weir contacts the team through the Stargate soon, however, and sends a team to help. It seems as though the members of the Atlantis expedition and Jamus have been saved; however, the team cannot possibly save over a thousand people. Jamus, fiercely defiant, states that he will not go without his people — and will make sure that the Atlantis team does not, either. He takes Teyla as a hostage, and will only release her if Sheppard gives his people safe passage off the failing station. As way of explaining his refusal to abandon them, he describes to Teyla his people’s actions to keep the Wraith away – they used atomic weapons to destroy the incoming Wraith fleet, counting on the radiation from the weapons to sterilize the planet, eliminating the Wraith’s desire to feed upon the people any longer – but eliminating the people themselves at the same time. All survivors of the culling were killed by the radiation, making the planet seem useless to the Wraith, and thus ensuring that the survivors aboard the space station would no longer have to deal with the threat of culling.

Teyla and the team cannot guarantee the survival of the people in stasis, so Jamus takes Teyla hostage; he places her in stasis, along with himself, and McKay is unable to distinguish her life-signs from the survivors already in the device. He is also unable to devise a way of interfacing the storage system’s power needs with a Puddle Jumper’s systems in the time remaining, so Sheppard, determined to try to save Teyla’s life, develops a plan to pilot the shuttle down to the planet’s surface with the stasis unit aboard. As all of the fuel in the shuttle was used up by Herick in his suicide, Sheppard cannot get the shuttle into orbit; he tries to align the vessel for reentry, but at the critical moment, the shuttle’s explosive bolts fail, keeping it attached to the station. Sheppard rides out a great deal of turbulence before the moon breaks up around him; he pilots the ship to a rough but safe landing. Both he and the stasis unit survive; eventually, everyone within it (including Teyla) is safely awakened. Unfortunately, due to his injuries, Jamus does not survive the awakening process. Teyla remarks that Jamus was only doing what he thought was best for his people, and that in his position, Sheppard would have done the exact same thing – to which he objects.

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For two years, John Sheppard and Dr. Rodney McKay have been playing a computer game left by the Ancients, in which they each develop countries on opposite sides of a river in competition with one another (much like the video game Populous). While McKay has been pushing his country (”Geldar”, named after a former romantic interest of McKay’s) to develop technologically, Sheppard has been encouraging his (”Hallona”, named by the Ancients who created it) to develop its military.

On a routine survey mission, however, a team from Atlantis discovers that it is not, in fact, a game. Their countries, and all the people in them, are real; living on a planet somewhere in the Pegasus Galaxy. With a satellite network in orbit to track their development and Ancient technology to receive the “players’” instructions, their civilization has, in fact, been a Lantean social experiment. The team has stumbled upon McKay’s country (easily identifiable by the multitude of paintings of his face throughout the village), they go to the planet to investigate.

The team visits Geldar first, where they are met by Nola; she immediately recognizes McKay as their “Oracle”, and explains that their people were given life thousands of years ago and guided by the Oracle through a console, but then all communications suddenly ceased — interrupted by the war with the Wraith. Unknowingly, McKay and Sheppard have picked up where they left off.

While McKay stays with Nola, Sheppard takes Teyla and Ronon to visit “his” civilization, located across the river. There they meet Baden, the aggressive leader of Hallona. He reveals that at the command of Geldar’s Oracle, the Geldarans have begun mining for valuable coal under his country. He believes that the proper response is to launch an attack.

The two leaders are brought back to Atlantis to learn about the Ancient technology and to have their dispute mediated by Dr. Elizabeth Weir, but they refuse to cooperate. Tensions are high, and as a result of Sheppard and McKay’s “game”, the two peoples now stand on the brink of war. Despite their best attempts, neither Weir, McKay, nor Sheppard can convince them to make peace, and things quickly escalate into an all-out attack.

On both sides, it soon seems as if the other side has achieved total victory. Geldar is seemingly overrun by the larger Hallonan army and its people slaughtered, while Hallona seems to have been devastated by Geldaran bombing runs (completed by use of dirigibles). After both sides admit defeat, McKay and Sheppard reveal to their respective countries that the whole display was a ruse in order to show them how costly a war could be. The Daedalus, having arrived earlier in expectation of the conflict, was transmitting fake data to each control console while using precision attacks to simulate the damage outside. It seems as though a peace has been achieved, and both civilizations set out on their own, no longer constrained by the game – which has now been deactivated and sealed at Weir’s command.

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In order to conserve power, Rodney McKay and a scientist crew (including Zelenka) are heading through a recently flooded area of the city, shutting down systems recently activated by the ancients during their short period of controlling the city.

Rodney powers up the machine and is suddenly surrounded and circled by a giant spiral of what appears to be DNA or some sort of energy (then subsequently gets hit by bolts of electricity from the machine) and stands there, surprised. Everything appears normal, except for the fact that Rodney just survived a few lightning strikes with no damage to his body.

Later, Rodney discovers that his hearing has improved greatly, and he overhears the team talking about him, so he grabs his tablet, which has moved across the table into his hands, and walks over there and has a very minor rant. An announcement comes over the Atlantis PA system calling Colonel Sheppard and his team to the gateroom/control room. There they receive a transmission from Major Lorne’s team. They are under attack with enemy soldiers closing in fast. After they head out to start the rescue, Zelenka talks to Dr. Weir. He has discovered that the device is designed to manipulate human DNA (a DNA Resequencer, presumably)

Sheppard’s team returns with Major Lorne and according to Rodney, the enemy attacking Lorne’s team were defeated when Rodney “thought ‘wouldn’t it be great if all their weapons jammed all at once?’ and then it just happened”. Dr. Weir, of course, does not believe him, and neither does anyone else, so to prove it, he uses his telekinesis to pick up Carson Beckett right off the floor. Everyone stares at Rodney. Weir tells Rodney to put him down, which he promptly does.

Rodney is in the infirmary on a bed, hooked up to a vitals monitor, and a few other machines. Apparently there is a dramatic increase in synaptic interaction throughout all the sections of the brain, much higher than normal levels. Weir mentions an incident at the S.G.C (Stargate Command) “just over a year ago” where they found a highly evolved being in stasis, caused by altering of the DNA by a DNA Resequencer by a Goa’uld named Anubis, designed to artificially accelerate the human physiology to the point of ascension.

Rodney stays a while in the infirmary, and then is let out with Ronon Dex keeping him company. He discovers he can read people’s minds, so he heads to Dr. Weir’s office and ‘asks’ permission to utilize the control chair of the city and reconfigure the power systems to increase the efficiency of the ZPM, as it will dramatically lower the city’s power usage, and thus increase the ZPM’s life. While he is fiddling with it, the lights in the DNA Resequencer lab where Zelenka is trying to fix the device (it was damaged in the initial explosions/lightning when Rodney had his DNA resequenced), go out. He heads to the control chair room to talk to Rodney, but Rodney is arrogant and keeps working. Zelenka heads back to the lab, very angry at Rodney. Weir is going over the research log that the Ancients left behind, in her office, when Sheppard walks in and asks how she’s going with it, she says she’s just getting to what she thinks might be the “good bit”. Sheppard leaves, but before he goes, Weir says that they need to talk to Rodney right away.

They walk into the control chair room and Rodney reads their minds. He realizes what is happening: If he does not ascend near the peak of the evolution, he will die soon afterwards. He is faced with a choice: Ascend or die. At this point, a massive power surge starts going through the city – Zelenka is struck by a bolt of electricity and badly wounded. He is rushed to the infirmary and has a massive wound, in very unstable and critical condition, with no pulse. Beckett prepares the paddles. Rodney tells Beckett to “MOVE!” and Beckett protests that “the man is dying!” and Rodney says “I know, just give me a second”. A look of concentration comes over Rodney’s face as he puts his hands above the wound. It begins to heal very quickly. In a few seconds the wound is gone. When the wound is healed, Rodney is amazed that he could do it. In a panic, he runs out of the infirmary; probably scared of what other powers he has and to continue his scientific research into greater technologies.

Rodney goes on an inventing spree, inventing a new type of math, a way to increase the shield power on the Daedalus and designing a hyperdrive prototype for the Puddle Jumper.

Rodney goes through some emotional changes, realizing his fate is coming; he takes meditating lessons with Sheppard, who learned from the Ascension-seeking villagers he was trapped with in Epiphany, so that he will be ready when the time comes. He apologizes to Zelenka for being very mean to him during the past few years, and even calls him a “brilliant scientist”. Zelenka is touched, and even a little confused as Rodney walks away.

Rodney also speaks with Teyla and helps her with the “tea ceremony for the anniversary of her father’s death.” He comments that “I know you’re not supposed to do it alone.” Teyla appreciates this sudden and strange show of compassion and caring. He then finds Ronon and asks him about the scars on his back from the Wraith. He asks, “Are those like a badge of honour or just a constant reminder of something you’d rather forget?”. Ronon responds “I try not to let the things I can’t change bother me”. Rodney hugs Ronon and squeezes him tightly for a few seconds, and then says “Hope you don’t mind… I just healed them.” He also typed out a 500 page book for Elizabeth of all the “good things [she's] done”.

Eventually Rodney ends up back in the infirmary, as his body starts to die: the advanced cerebral cortex is affecting the lower functions of the brain and his body is losing its natural ability to keep itself alive. Rodney and Sheppard have another go at the meditation, and Rodney slowly sinks to the required level of activity.

He slowly goes to 1 Hz and suddenly his eyes open and he grabs Beckett violently. He lets him go and relaxes back into the bed. No pulse. Beckett says they need to bag him and get him on the ventilator. Weir protests, saying “He gave us strict orders to – ” and Beckett cuts in “No, you don’t understand. He just told me how to save him.”

At the lab, they place Rodney in front of the controls, where he was resequenced before. The machine is turned on, and Rodney is returned to normal. Apparently (according to the now normal McKay) “The device was designed to manipulate your DNA, and it couldn’t reverse the evolutionary process because everyone’s DNA was different, it makes certain changes that cause the DNA to evolve, in-in ways specific to your own unique physiology.” Zelenka cuts in: “In order to manipulate the DNA to its previous state, the program required a precise reference point.” Beckett says “Fortunately we keep blood samples from all the Atlantis team members for base-length comparisons.”

Rodney is back to normal, and is no longer “a dead man”, however he has regrettably lost all his newfound powers, including the ability to understand the theoretical work he did while he was “advanced”.

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Atlantis receives news that a village on another planet is protected by a hero with superhuman strength. Colonel John Sheppard and his team visit the planet, only to realize that this hero is really Lucius Lavin. The team suspects that he is using the same drug he used on Atlantis that caused everyone near him to obsessively like him. Lucius says that he doesn’t need the drug because he has a Personal shield emitter which makes him invincible, and won the hearts of the villagers after taking out some troublemakers; he maintains their devotion by claiming credit for some of the heroics that he read about in Atlantis’s mission reports.

While Lucius is hiking in the nearby woods, a small group of thugs with rifles invade the village, asking for the “hero.” With weapons raised, the gang’s leader, Haemon, asks Sheppard whether he is the rumored hero who will stop them from robbing the town and burning it to the ground. Lucius Lavin arrives with an air of triumph, declaring that he is the hero and will protect the village. The thugs’ blows bounce off his shield, and he makes quick work of them.

The team visits with Lucius in his new home, but after saying goodbye, they decide to stick around and see if they can learn what Lucius is up to this time. They follow him to a secret meeting with Haemon and his men, learning that Lucius hired them to stage the attack, and that he is paying them less than what they agreed to, despite having legitimately injured two of them. The men are furious – they are proud soldiers of the Genii, former members of Cowen’s personal guard, who were forced to work for hire after Ladon Radim’s coup (”Coup D’etat”).

When Lucius returns to the village, the team tries to expose Lucius’s con to the villagers, but the villagers do not believe them. Later, Acastus Kolya and some of his soldiers arrive, looking for Sheppard. The team realizes that they can’t fight Kolya without risking the lives of the villagers, so with the help of Lucius, they hide in a closet until Kolya leaves. Lucius confronts Kolya and orders him to leave; Kolya’s shots bounce off the shield, but Kolya soon realizes that he can torture Lucius by trying to drown him. Lucius gives away the team’s location, but they have relocated.

Kolya ties Lucius to a chair and tries to get more information from him. Lucius repeats his false heroics to Kolya and his men, who prove uninterested. Kolya leaves Lucius to deal with some other work. Sheppard’s team sneak in and try to break Lucius free, but make a desperate premature exit when a bomb strapped to Lucius’s chair goes off. The team is immediately captured by Kolya, except for Sheppard who manages to escape.

While Kolya and his men search for Sheppard, Lucius sneaks away and finds him first. Kolya radios Sheppard to tell him that the stargate is heavily guarded, and that he will kill members of the team unless Sheppard surrenders. Lucius returns to the village and secretly meets up with the villagers, convincing them that they should fend for themselves: if they always depend on one person to protect them, then they are giving up their freedoms.

Sheppard shows himself to Kolya. Kolya immediately orders his men to open fire; Sheppard is wearing Lucius’s personal shield, but it runs out of power after the first barrage. Lucius shows up with the villagers, who overwhelm Kolya and his men. Kolya, not wanting to surrender, duels with Sheppard and is killed.

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Dr. Zelenka, Ronon, and John Sheppard are in a Puddle Jumper returning from an expedition on the mainland to document and hunt local fauna. As they return, Zelenka notices that Atlantis does not appear on the sensors properly. After adjusting their direction by forty degrees they are on the proper course towards Atlantis again.

Teyla Emmagan begins to see repeat visions of Ancients on Atlantis. First she is assumed to be under stress, but after a while other people in the city begin to see the same visions.

A large Flagisallus passes the Puddle Jumper.

Meanwhile, McKay and Sheppard notice a sea creature which Rodney has named “Sam” (after Samantha Carter), because he believes it to be the same one that led Sheppard and Zelenka to rescue McKay from a damaged Jumper on the ocean floor. After using Atlantis’ sensors to find another of the sea creatures, much larger than “Sam”, they decide to take a Puddle Jumper to investigate closer. During a close encounter with the sea creatures, Sheppard and McKay develop intense headaches and McKay falls unconscious.

In the infirmary, Zelenka explains that the sea creatures emit a low frequency pulse and an electromagnetic field which, in combination, are very dangerous to humans. Very soon, most of the city is affected by this. Many victims are transported to the Daedalus, now orbiting the planet, but there are too many in the city to all be relocated.

During his recovery, McKay uses his tablet to locate an Ancient bio-lab dedicated to studying the native marine life and manages to translate what the whales are saying. The Atlantean whales are warning that the sun is about to send out a gigantic coronal mass ejection (similar to a solar flare) straight at the Lantean planet and although the shield will protect Atlantis, the radiation wave will kill all plant and animal life on the planet and destroy the atmosphere, thereby depleting any breathable oxygen. The whales are congregating underneath Atlantis’ shield for protection.

The vision of a Lantean trying to help the burned pilot of the Adaris.

The visions that people have been seeing are a genetic memory that the whales have of this catastrophe, which happens every 15,000 years. The Lanteans were experimenting with communicating with these creatures when this traumatic event occurred. An Ancient ship was near to the sun when the ejection began and most of its crew were killed immediately by the radiation. The pilot managed to jump to hyperspace and overtake the radiation wave before it reached Atlantis and warn the people there.

The Daedalus is hit by the coronal mass ejection.

Now knowing what is happening, the team consult the Ancient database and discover that the last time this happened the Ancients managed to temporarily expand the city’s shield to encompass a large percentage of the planets surface. Unfortunately, with only one functioning ZPM, McKay is only able to expand the shield by a radius of a few kilometers.

In order to save Atlantis as well as the planet, Sheppard comes up with the idea to transfer the ZPM to the Daedalus and move the ship into position between the sun and the planet. When the coronal mass ejection begins, the shields aboard the Daedalus (boosted by the ZPM) successfully deflect the emission away from the planet, with the Daedalus sustaining only minor thermal damage in the attempt.

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Woolsey and O’Neill are hiding out in a section of the city where the sensors are not working when Sheppard’s team comes through the gate, taking fire from the Asurans. Sheppard contacts the two and tells them to stay put, dropping an explosive device into Stargate Operations before piloting the Jumper through the window directly behind the gate. The device detonates, damaging critical systems and all but destroying the upper section of the central spire. With the critical systems, including sensors, destroyed, the Asurans attempt to repair the damage. They are also aware of Sheppard’s message, and because they had killed all of the Lanteans, suspect that there are humans hiding within Atlantis.

The team then take the Jumper to retrieve Niam, who is still floating in space where they left him (”Progeny”). McKay plans to use Niam to transmit a program that will make all the Asurans freeze, allowing them to finish them off with the ARGs. Niam has been damaged by his long exposure to vacuum and solar radiation, and is unconscious. McKay begins uploading the program but notes that they need to be very close to the city in order to make it work. Any attempts to extend the program’s range would mean increasing Niam’s power levels, which risks reactivating him.

When the Jumper returns to Atlantis, it is attacked by drone weapons. Sheppard maneuvers the Jumper between the city buildings but cannot shake them. He takes the Jumper into the ocean, heading for an underwater docking bay. However, the bay will not repressurize, and due to the damage taken earlier, the Jumper is taking on water. They radio O’Neill for help, and he swims down to the docking bay control room, holding down a dead man’s switch to drain the docking bay while Woolsey keeps a lookout. O’Neill succeeds, but an Asuran search party finds and captures both him and Woolsey.

McKay continues to work on Niam, as the others discover that O’Neill and Woolsey have been taken, possibly to be mind-probed. This is indeed the case, and having discovered Sheppard’s plan, the Asurans reactivate Niam, forcing McKay to destroy him with an ARG. With “Plan A” gone, Ronon suggests they simply go on a killing spree with the ARGs but McKay warns them that eventually the Asurans will determine the frequency the disruptors use and develop an immunity. McKay comes up with another plan and asks Sheppard how much C-4 they have.

The team splits into three groups, each going to different shield control units around the city. Sheppard and McKay go to the cell where O’Neill and Woolsey are being kept. McKay tells the two captives that the plan is to disable the city’s shield emitters with C-4, allowing the Daedelus to beam nuclear bombs directly into the city and vaporize it after they get away. However, McKay is apparently unable to override the coded lock to free them, and he and Sheppard are forced to leave.

The Asurans finish repairs to Stargate Operations and, with the city now being powered by ZPMs, activate the city’s Stardrive. Beckett and Teyla head to the chair room where Beckett launches drones to damage the stardrive. The Asurans, however, have extracted information about the plan from Woolsey’s mind, and capture Sheppard’s team just as the last of the C-4 is planted. The Asurans remove the C-4 and gloat to Sheppard that the humans’ plan has failed. Detecting the Daedelus entering orbit, the Asurans raise the shield…

…and, in flashback, McKay describes his plan to Sheppard: to insert the disruptor crystals from the ARGs into the shield control units, turning the Atlantis shield into a giant disruptor weapon. A fake plan is told to Woolsey and O’Neill to feed disinformation to the Asurans and the C-4 left as misdirection. When the Asurans activate the shield they are destroyed in one fell swoop. At the last second the team contacts the Daedalus and convinces Col. Steven Caldwell not to destroy the city.

The city recaptured, the Atlantis expedition moves back in, and with O’Neill and Woolsey’s approval Weir will once again be in command.

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