Rodney has returned to Atlantis and Weir orders the self-destruct activation. As they attempt to dial the Alpha site, the gate is suddenly activated; the wormhole was established from Earth. Much to everyone’s amazement, a company of marines come through and Weir and the others are greeted by Col. Everett who instantly takes over command. He informs them that they are here to defend Atlantis at all cost, and that they have brought weapons and equipment with which to do so. Rodney concludes that Stargate Command found a ZPM and Everett informs him that the Daedalus will arrive in four days with it.

In the conference room Everett informs the others about their plan, but Weir is only allowed to join after Sheppard insists. They are informed that they will use advanced railgun weapons originally intended for use on Prometheus, and eight Naquadah-enhanced 1200-megatonne nuclear weapons as stealth space mines. Along with these, they have brought a Mark II Naquadah generator, which is capable of a 600% power increase over Atlantis’ Mark I reactors, and was designed to power the City’s Weapons Chair. After the meeting, the railguns are deployed and the mines are laid in space by cloaked Puddle Jumpers. Meanwhile Everett visits Teyla in the training room and orders her to stay out of the way, cementing the distrust surrounding her.

After considerable tinkering, McKay is able to link the new reactor to the weapons chair, and the platform is activated by Beckett. McKay subsequently discovers that there are only a few dozen Drone Weapons left. The remaining multi-thousand were used during the original siege 10,000 years previously. Without warning, there is an alarm; the deep-space sensors have detected hundreds of asteroids heading straight towards the proximity-activated nuclear bombs. McKay assesses that the rocks were launched by the Wraith, who have somehow discovered the mines. With no way to deactivate the warheads, the locater signals of all eight warheads vanish on the display as the mines detonate, with the Wraith at a safe distance. The radiation causes interference that disables the sensors.

Later Col. Everett meets with Sheppard in the holographic archive and Sheppard grimly plays the history of the galaxy. Everett then informs him that he read the report Sheppard submitted surrounding the events in Rising. He explains that Col. Marshall Sumner was a personal friend of his and that he is outraged with Sheppard for killing Sumner. Suddenly they are informed that there are approaching Wraith darts and the battle for the city starts. Marines man the railguns and Sheppard takes the Chair; thanks to the Drone weapons and the railguns the first wave of Darts are destroyed but some parts of the city are hit.

Contemplating strategies, Sheppard suggests that they remotely control the Puddle Jumpers using the Chair and fly them, cloaked, into the hive ships armed with an explosive; he believes they should ask the Genii to use their nuclear weapons. Suddenly Teyla enters and informs them that there are Wraith in the city, who had invaded during the first wave. Together with a group of Athosians, the military starts to search for them. Meanwhile Weir gates to the Genii world, but is captured by them and held hostage. They want to exchange her for the C-4 they have been cheated out of, however Weir is able to convince them that they will use the C-4 only to test the devices, while they could be used for their true purpose of destroying the Wraith. The Genii finally agree and supply the Atlantis team with two nuclear devices. The hunt for the Wraith is going badly, as the Wraith have begun damaging and destroying the naqahdah generators powering the City. To make matters worse, McKay soon discovers that the Genii nukes are incomplete; he and Zelenka are soon in a lab completing the weapons against their fatigue, much to Beckett’s disagreement.

At Atlantis the test-run of Sheppard’s plan is a success, so McKay and Zelenka start to install the completed weapons into the Jumpers. Meanwhile several men are taken out by the Wraith and the wounded are taken to the Alpha site. A second wave of Darts appears without warning; Sheppard mans the control chair to take control of the Jumpers. After several attempts at initializing the Chair, McKay realizes the reactor has depleted its supply of naqahdah. Desperate, Sheppard decides to fly the Jumper himself in a hive-ship, much to the shock of Weir.

As Weir cannot stop him, Sheppard rushes to the Jumper Bay and takes it up. Outside, as Ford’s team attempt to repel the Darts, a group of Wraith materializes in front of them. Someone lets off a grenade, and Ford and a Wraith are catapulted into the ocean. Inside, Everett’s team is overrun and he is cornered by a Wraith. Out of ammo, the alien begins to feed off him. The final scene of season one sees Sheppard heading undetected into the Hive’s Dart Bay, the nuke armed, while back in the control room, Rodney counts down until detonation.

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While the Wraith come closer to Atlantis, the leading group of the expedition is informed by Dr. McKay and Dr. Zelenka that the Wraith will pass the last Ancient defense satellite; they are very confident can bring it back online and obliterate all three Hive Ships before they even reach Atlantis. McKay volunteers for the mission, and while he packs up he talks with Dr. Zelenka, who tells McKay that he should go and they even start to quarrel about it. Meanwhile Elizabeth Weir, John Sheppard and Bates search for a new Alpha site; afterwards Bates tells Sheppard that he doesn’t trust Teyla but Sheppard defends his team member.

Weir is informed by Dr. Zelenka about the self-destruct of the city (mentioned in Hide and Seek as overloading the naqahdah generators) and that it wouldn’t destroy enough of the city. He shows Weir a simulation which predicts that the Wraith will be able to recover some of the City’s technology, and some of the database. Weir realises they have to find a way to delete the Ancients database so that the Wraith cannot recover it. Suddenly the Stargate is activated and Sheppard’s team comes back. Bates assumes they were attacked by the Wraith and immediately accuses Teyla, but Sheppard then says they were attacked by some kind of T-Rex. Later Teyla confronts Bates and they start to fight (with Teyla actually punching Bates in the face) until Sheppard and Lt. Ford intervene.

Meanwhile in space, the Puddle Jumper approaches the satellite and McKay enters it, wearing a spacesuit, to reactivate it. He is successful in using a Naquadah generator to power up the maintenance systems, creating an atmosphere that allows Dr. Peter Grodin and the Jumper’s pilot to enter and assist with repairing the weapon, although Grodin inadvertently activates the gravity system while McKay is several feet in the air. After frustrated diagnostics, they discover that power connectors linking the weapon’s energy storage buffer to the main firing system have been damaged, but to solve it someone must go outside the satellite. After drawing the short straw and much protest, McKay goes EVA. He discovers that meteor strikes have severed the connections, determines that he can reroute the power and finally is able to repair it. However, McKay has inadvertently rerouted power away from the Jumper dock, meaning they cannot dock with the satellite nor take Grodin back on board. Grodin realises there is no time to repair the fault, and he decides to stay on the satellite. This proves useful, as he will be able to keep the power levels as low as possible, ensuring the Wraith cannot detect the active system before it is ready to fire, and also to repair it if there is a problem.

At Atlantis Halling visits Weir and tells her that he doesn’t want Atlantis to be destroyed. However, she tells him that she has to protect Earth. Later Weir is informed by Zelenka that he invented a virus to delete the database and Weir wants him to make a backup of it in the hard-drive they brought from Earth but he tells her that they only can save about 8%. Meanwhile Sheppard and Ford search for more potential Alpha sites until they are called because Bates was attacked and badly wounded. They ask Teyla about it but she tells them that it wasn’t her.

They discuss with Weir who it could be but then Dr. Beckett finds out that there is a Wraith in the city. With a biometric sensor they are able to find out where the Wraith is and they try to capture him. However, the Wraith is able to take out Sheppard’s team until he is stunned by Ford. The Wraith is imprisoned and Sheppard starts to interrogate him after he named him Bob but he keeps silent. Teyla decides to start communicate telepathically with him but he overwhelms her. Sheppard fires with his gun at him several times, wounding him badly.

Meanwhile the Wraith Hive-Ships drop out of hyperspace as predicted, and Grodin powers up the satellite. McKay watches from the cloaked Jumper as the energy beam from the weapon successfully slices through and destroys one Hive-ship. Amid the celebration, Grodin radioes that he is having trouble – McKay’s rerouting has overloaded and the weapon can’t be fired again. Grodin cannot bring it back online, and as McKay orders the pilot to rescue him, the remaining Hive Ships destroy the satellite, killing Grodin. McKay can’t do anything, thus he informs Weir and is ordered to return to Atlantis. Weir informs the base about what has happened and afterwards starts the self-destruct countdown. Having heard the evacuation order, Bob tells them no matter where they go, no matter where they hide, the Wraith will find them, as well as Earth. A frustrated Sheppard finally kills him.

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It is night in Atlantis. While most of the people sleep, a Wraith walks through the corridors, enters Teyla’s room and attacks her. She then wakes up as it was only a dream. On the next day she trains with Major Sheppard but because she isn’t concentrating she is defeated. Later a meeting is held where the leading members of the expedition take part and it is discussed what they can do however there seems to be little hope. During the meeting Teyla also aggressively speaks to Dr. Weir much to Sheppard’s surprise.

Later Teyla meets Kate Heightmeyer and when the doctor wants to talk with her, Teyla isn’t interested and becomes angry when she concludes that Sheppard talked with Heightmeyer first about her. She confronts the Major but he only wanted to help her and even forbids her to come with him to the Alpha Site. She then wants to take a nap but because she can’t sleep she visits Dr. Heightmeyer. They talk about Teyla’s ability to feel the Wraith and she tells her more about it and even reveals that there are other people like her who can feel the Wraith but her sense is one of the strongest. After another nightmare Teyla again talks with Dr. Heightmeyer and afterwards she visits Dr. Beckett to find out if it’s perhaps a biological problem. They then decide to go to the mainland to find out more about her.

On the mainland Teyla visits an old woman named Charin with whom she talks about her past and her abilities to feel the Wraith. After some hesitation Charin tells her a story about some people from another planet who returned after the Wraith captured them. However they were forever changed and began to hear voices. Because of this, many of them either left though the Stargate or were killed. It turns out that Teyla is a descendant from these people and with approval from Dr. Weir, Sheppard’s team flies to the planet. On the they find a Wraith laboratory which only Teyla can enter at first. Inside the laboratory, the team finds a data storage device which holds a lot of information. Weir is partially able to translate the information since the language seems to be derived from the language of the Ancients, meaning that the Wraith evolved in Pegasus after the Ancients arrived. As it turns out the Wraith are related to the Iratus bug that attached itself to Sheppard. Over several centuries, the Iratus bug had absorbed enough human DNA to evolve its own genetic makeup and create the Wraith species the team, and the Ancients before them, were now fighting. She then does some researches with Dr. Beckett.

On the next day Teyla is informed by Weir and Beckett that a lonely Wraith experimented with some people to make the food more compatible to the feeding process against the wishes of the others and it turns out that Teyla has a small bit of Wraith DNA inside her. While Teyla again talks with Heightmeyer the leading team discusses about her and Weir later finds out that the Wraith scientist stopped because his experiments gave the people the mental abilities of the Wraith who then could hear what the Wraith said. With no way around this, he released them back to their home thinking that interbreeding could dilute the effect. When the others found out what he did, they wiped out the people on the planet. They then conclude that Teyla may be able to get some information from the Wraith.

After some discussion with Dr. Weir and Heightmeyer she agrees to try it. During the first run she is able to see what a Wraith sees but when the Wraith feeds on a man she stops. She later again tries to find out more but this time a Wraith takes control over her telling them they are fools and they stop. Suddenly the Stargate activates and Sgt. Bates returns since the Wraith attacked the Alpha site as if they knew they were there.

Later Lt. Ford talks with Teyla and she again wants to try it. She does so but again a Wraith takes control of and she wounds Dr. Beckett until she is shot down by Bates (who doesn’t trust Teyla after the incident with the Alpha site) with a Wraith stunner. After she wakes up she apologizes and also reveals that the Wraith come here to get access to a new rich feeding ground – Earth. They realised that the female Wraith wasn’t only feasting on Sumner, she was interrogating him.

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After Atlantis discovers three Wraith Hive-Ships coming in their direction, the leading team discusses what to do. Lt. Ford suggests they take the ZPM from M7G-677 but Dr. Weir refuses to back such a suggestion. McKay reveals that they can use the whole of their energy resources to open a wormhole to Earth and send a high-compression data burst. Though risky, the team decides to do it. After the meeting, Dr. Zelenka informs the team where the Hive-ships will leave hyperspace and Maj. Sheppard and Teyla decide to personally oversee the threat. They travel to a planet which Teyla knows via Puddle Jumper and meet an old friend of hers named Orin. After warning him of the threat from the Wraith, Teyla tells Orin that they will rescue his family although Sheppard can make no promises.

At Atlantis, McKay suggests that since space will remain after the initial data transfer, everyone should include a personal message to be sent to Earth as well. Weir decides that every member of the team should have the possibility to send a video message to their loved ones (given they do not reveal classified information). Ford takes on this task by filming a message intended for his grandparents.

Meanwhile, Teyla and Sheppard quarrel about what Teyla’s promise of help to Orin when the Wraith abruptly appear. Each hive ship is escorted by three cruisers, making the force invading Atlantis much worse than expected. They shower the planet with a flurry of Wraith darts. Before the puddle jumper can escape through the Stargate, it is dialed by the Wraith so they return to the predetermined location to meet Orin and wait for him.

In the meantime, the Atlantis members continue to forge their messages. Dr. Beckett, although inarticulate at first, sends a sentimental message to his mother. Dr. Zelenka recounts (in Czech) Atlantis’ Rising. Sgt. Bates sends a message to his younger brother and Dr. Weir informs the families of fallen servicemen about the fate of their family members as well as an ulterior personal message. Dr. McKay even films a lengthy message on his own while Dr. Kavanagh sends a message to Gen. O’Neill in which he lists all the mistakes Weir has made (in his opinion). During these clips, several flashbacks occur from former episodes which outline ambiguous details and facilitate a clearer understanding of the past months; including the events during the storm around Atlantis, the attack of the Genii, and several battles with the Wraith.

On the planet, Sheppard and Teyla can only watch in horror while the Wraith cull the population. Suddenly, a strange beam slams into the village so Sheppard resolves to investigate. While he is away, a Wraith passes by the jumper, oblivious to its presence. However, Teyla is able to collect inhabitants who wander by. When Sheppard returns, he adamantly wants to escape (since the gate is deactivated) but decides to wait on the mainland for Orin. Finally, he arrives accompanied by several other denizens, and Sheppard decides to take as many as possible aboard the jumper. They are able to flee through the gate but not without some human loss to the Wraith.

In Atlantis, Sheppard and Teyla divulge to Weir the threat which the fleet poses. Soon after, Weir asks him to record a message to the family of Col. Sumner which he promptly carries out. The “intergalactic e-mail” is successfully sent to Stargate Command, received by Lt. Col. Carter.

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Back at Atlantis, Dr. Zelenka has discovered new long range scanners, which can track objects into deep space. It has activated because of a Wraith dart inbound for the planet.

When they finally locate the place where the object is hiding, an old Genii enemy, Kolya appears in the scene to sabotage their plans. They realize that one stone (out of nine) is missing for them to activate the release mechanism.

They get back to a previous location where Rodney finds the missing stone. In the meantime, Sheppard and Teyla had managed to prepare a little bit, so when Kolya and team arrive, they are ready. After a member of Kolya’s team dies by placing his hands in the device that would release the ZPM, Rodney and Sheppard realize that the stones need to be arranged on a particular pattern, so that they add up to 15.

On Atlantis, three puddle jumpers have been scrambled. One is destroyed, while the dart begins to scan the city. After completing its mission, it self destructs.

Back on the planet, once the stones are rearranged, they are able to release the ZPM. Taking advantage of Kolya’s distraction, Teyla, Sheppard and Ford get control of the situation. Kolya tells Sheppard that the reasonable thing to do was to kill him. Sheppard tells him that it would and if he ever interfered again, he would.

They leave the place with the ZPM, but when they are halfway to the Jumper, a group of locals surround them and they have to give away the ZPM: the woman that had been helping so far was in fact the leader of the Brotherhood. They try to reason with her, but since Rodney had already commented that they were not from Atlantis but from Earth, the locals believe that the Ancients are going to return in the future. Until then, they going to hid the ZPM on another world.

Back at Atlantis, the team updates Elizabeth Weir, who tells them about the dart. Zelenka also reveals that the dart sent its information into deep space to three hive ships, which will arrive at Atlantis in two weeks.

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McKay believes that the Ancient is in some sort of stasis, slowly aging but she will eventually die since she is already very old. Despite Dr. Beckett’s protests Weir decides to awaken the woman to ask if she knew where any ZPMs were left. When she later wakes up she at first isn’t saying anything, but she is listening and looking at them. Afterwards her only words are “It worked.” until she falls asleep. Also the team finds a piece of paper with Stargate addresses written on it, including one they already been to, M7G-677. Later when the woman wakes up, she claims that she is Elizabeth Weir from an alternate timeline who travelled through time in the past. Carson runs a DNA test on her and confirms her words, while McKay finds out that they nearly killed her when they arrived at Atlantis and cut off power to the systems that were attempting to revive her.

Later when old Weir awakes again she starts to tell her story: when her team arrived at Atlantis only the lights went on but not the consoles of the computer which is different from what happened in the current timeline. When McKay tells her this old Weir falls asleep again and when she wakes up she is brought into the conference room. There she tells how the shield of Atlantis broke down almost immediately after their arrival in the city which caused Col. Sumner and many others to drown. Also the city had no fail-safe to rise to the top of the ocean so the city slowly collapsed. In the gateroom, Rodney died by drowning. Before water engulfed the city, Weir, Sheppard and Dr. Zelenka managed to get into a Puddle Jumper that is different from the others. The pod was somehow beamed into space above the planet, where the time travel device in the Jumper was activated, causing it to go back in time 10,000 years. They were then attacked by two unknown ships (Wraith darts). Hoping for a chance to retaliate, Sheppard inadvertently activated the weapons systems, but was only able to destroy one Dart before being shot down. When Weir woke up, she was back in Atlantis, treated by a man named Janus who informed her that Sheppard and Zelenka didn’t make it. She then found out that she went back in time 10,000 years. The Atlanteans then informed her of war with the Wraith; despite their more advanced technology, the Wraith are overwhelming them with sheer numbers.

Weir was later brought before the council and she asked if they would give her a ZPM, and use the time machine to send her back to the precise moment when her team arrived through the gate, but they refused. They then ordered the time machine destroyed, and offered her to join them in returning to Earth. Only Janus, the inventor of the time-travelling Puddle Jumper, helped her. He informed her that the power generation capabilities of the city might be extended by using a single ZPM at a time, as opposed to the normal configuration of all three simultaneously. He devised a fail-safe to allow the city to rise should his plan fail and power drain to a critical level, and placed Dr. Weir in a stasis pod. The pod is set to bring her out of hibernation every 3,300 years or so, enabling Dr. Weir to rotate the ZPMs over the next 10,000 years.

When all the Ancients left, Weir set the city to slumber and nervously went into stasis. Back in the present the young Weir thanks her and her older self tells her that the gate addresses on the piece of paper she had lead to Ancient outposts with ZPMs. Young Weir informs Rodney and Sheppard about it while back in the bed the old Weir dies. Later the young Weir sprinkles the ashes of her older self from the earthenware pot she got from the Athosians over the city.

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Chaya undergoes some tests at Atlantis. Sheppard shows her the city and talks about Earth. In the control room, Chaya suddenly activates a bio-detector, and everyone is stunned with the revelation that she has the ATA Gene. Later, in the conference room, they ask Chaya to accept refugees in exchange for advancements in technology for her civilization, but she declines. They then offer knowledge of their religions, which she agrees to review.

Sheppard decides to take Chaya out to a picnic dinner as a show of goodwill. After some talking, they kiss.

Later, Rodney talks with Sheppard and tells him he feels that something is different about Chaya. Carson has found that Chaya is in perfect health, much too perfect for a simple pre-technological society. Rodney is suspicious of Chaya, and concerned that Sheppard is forming such a close bond with her. Chaya overhears him and walks away.

Next morning, Rodney is busy scanning her as Chaya tells everyone that though she is fascinated by their religions, she cannot condone the hate and distrust that the people of Earth display for each other. She points out McKay specifically, especially after his comments of last night. Rodney suddenly realizes that she is an Ancient; she confirms his suspicions, and admits that she did not come to offer her help, but out of a romantic interest in Sheppard.

Before the conversation can go any further, she senses that the Wraith are attacking her planet. She turns into her Ascended form and leaves. Sheppard takes a Jumper and follows her back to Proculus. He takes out a few Darts and Chaya appears beside him and asks him to leave the battle. She turns into her Ascended form again and uses her power to destroy the Wraith forces.

Sheppard comes down to the planet and confronts Chaya. She explains that she is also Athar. Long ago, when the Wraith attacked her planet, she lashed out with one thought and destroyed them all. The Others punished her by restricting her to protecting Proculus only. If she tried anywhere else, she would be stopped. She had been alone for many years until she met Sheppard. After noting that Sheppard will still be permitted to visit her occasionally, she shares herself with him.

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While Dr. Carson Beckett and medical personnel attempt to discern the nature of the contagion, John Sheppard and Teyla Emmagan are training in the art of Bantos fighting. Sheppard begins to grow impatient, with Weir pointing out that there is nothing for him to do. Meanwhile, Beckett and his team have begun their work on checking out the team members—and prepping the victims for autopsy.

Sheppard receives word that Peterson, a member of the infected team, has escaped and is fleeing towards Stargate operations and, thus, the hub of the city. Against Weir’s orders, Sheppard orders Sergeant Bates to open the doors. Bates does so, offering an after-the-fact apology; “Doesn’t really matter now, does it?” replies Weir.

Sheppard manages to catch up with Peterson—who uses the transporter, ending up at the mess hall. Upon transporting to the mess hall, the city begins to lock down and control to the mainframe is broken. The only two people that can move around safely are Sheppard and Teyla, who procured hazmat suits from a lab. The city’s systems appear to recognize that the pair, being so equipped, are definite non-carriers who will be useful in the medical crisis and permit them free access throughout the city.

Meanwhile, results from the autopsies show that the victims died of a brain aneurysm above the visual cortex. As another team member begins to die, McKay theorizes that there must be more to the events. While the visual cortex can be affected, the frightening hallucinations are strikingly similar—to the point where there had to be another explanation. McKay and Beckett discover that the virus is not organic, but it is a work of nanotechnology. Shortly after this discovery, McKay runs out of time, but does not die. They theorize that the virus does not kill people with the ATA gene, which McKay received in an experiment. While it is designed to kill humans, it appears that the nanovirus is incapable of multiplying, thus limiting their effectiveness.

It was speculated that the nanites could be affected by an electromagnetic pulse. Sheppard goes to an EMP generator in McKay’s lab while Teyla goes to the mess hall to comfort the people there. Unfortunately, all doesn’t go as planned; the people in the mess area react violently, damaging Teyla’s suit in the process. According to McKay, the pulse wasn’t strong enough to destroy the nanites. With only 20 minutes until Ford and Dr. Zelenka die, Sheppard devises a plan to detonate a Naqahdah generator above the city. With McKay’s help in ironing out the details of the plan, Sheppard flies a Puddle Jumper, releasing the overloaded naqahdah generator 20 miles above the city. (The radiation fallout won’t affect the city at this distance, but the EM pulse will be devastating enough to incapacitate the nanites permanently.)

The plan works: the city rescinds the lockdown and the survey team can return to the main area of Atlantis.

While questions loom about who created the virus—it isn’t the Wraith, as they wouldn’t create a WMD to kill their foodsource and the Ancients would (theoretically) never reach that extreme; Weir firmly states to Sheppard that the clash in authority is something that should not occur again. Weir also firmly reminds him that Sheppard does not dictate what is and is not a military decision; that’s her call. While he reluctantly seems to concede the point, the question is raised as to whether or not this event will occur in the future.

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Sheppard’s team finds the Wraith ship dead and devoid of life, but are shocked to find evidence that indicates the Wraith crew of the ship resorted to cannibalism by feeding off each other – most likely out of desperation due to the lack of food supply on the barren desert planet. Further investigation of the ship reveals hundreds of stasis chambers for storing humans, thus indicating that the Wraith ship was actually a giant supply vessel.

Unknown to Sheppard and his team, a single Wraith from the ship’s original crew was still alive. The Wraith was not detected on any life sign scans because the Wraith was hibernating. Once Sheppard’s team entered the derelict Wraith ship, the ten thousand year old Wraith reawakened from hibernation and killed a scientist on Sheppard’s team and drained the life force another, Dr Gaul, but still left him alive. Leaving Dr. Gaul alive provides the Wraith with a tactical advantage, because it forces McKay and Sheppard to split up: one has to stay back to look after the weakened Dr. Gaul and instead of both going after the Wraith.

The Wraith finds the puddle jumper and Sheppard unsuccessfully tries, single-handedly, to reclaim the vehicle. Sheppard finds it impossible to kill the Wraith as the creature had survived for ten thousand years and therefore was a formidable opponent. The Wraith also possesses strong regenerative abilities because he had fed twice, very recently. Even when Sheppard unloads an entire magazine from his P90 submachine gun, the Wraith is only temporarily stunned before springing back to life. Not even a close quarters blast from a Wraith explosive device kills the creature or causes any kind of permanent injury.

The Wraith remains stranded on the planet, despite being in control of the puddle jumper, because it does not possess the Ancient gene and therefore cannot activate the vessel’s controls.

While Sheppard tries to retake the puddle jumper from the single Wraith, McKay stays with weakened and severely aged Dr. Gaul. During that time, Gaul tries to persuade McKay to go help Sheppard. McKay refuses to leave so Gaul takes the decision out of McKay’s hands by shooting himself.

In a last ditch effort to retake the puddle jumper, Sheppard distracts the Wraith with a flare and makes a dash for the puddle jumper only to be foiled when he bounces off the puddle jumper’s shields which the Wraith activated before it left the puddle jumper unattended. Sheppard’s failed plan causes the Wraith to smile. The Wraith then taunts Sheppard over the foolishness of his tactics – the Wraith’s military tactical senses had been sharped by over ten thousand years of survival on a barren desert planet, with nothing left to feed on but its own Wraith crew.

Out of ammunition, Sheppard engages the Wraith in a futile and short lived knife fight. The Wraith is about to kill Sheppard when McKay shows up and distracts the Wraith by shooting it. Sheppard and McKay continue to distract the Wraith until Ford and Teyla arrive in a second Puddle Jumper and are able to destroy the Wraith from space using a drone weapon.

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On the mainland, Carson increases the dampers and the storms passes them at high speed. Going into space, they make a reentry back into Atlantis. Teyla tells her Athosian friends to remain. They headed to armoury and Ford picks up a Wraith stunner in case they run into Sheppard.

While supervising McKay and Weir repair the grounding rod controls, Kolya contacts Sheppard and tells him if he doesn’t reactivate the generator powering the rod, they die. Sheppard was about to fix it when he was confronted by two Genii soldiers. They are stunned by Ford.

McKay finishes fixing the rod and tells Kolya that they must head back to the control room. When lightning strikes the city, it will course through the corridors. The control room is shielded.

The team knows the Genii will also be in the control room. Sheppard assures them that even the Jumper bay is shielded. They make a plan to defeat the Genii. Sora knocks out Carson and then fights Teyla to get revenge for her father’s death. Weir and McKay make a false attempt to activate the shield and tell Kolya they have to abandon Atlantis. Kolya decides to take the two with them because they would prove valuable. Sheppard and Ford surprise them, but Kolya holds Weir at gunpoint. Sheppard then shoots Kolya in the shoulder, causing him to release Weir and fall through the Stargate. Teyla won the fight and she and Sora helped Carson back to the control room. McKay activates the shield just before a deadly tidal wave hits Atlantis.

Everyone comes back and things return to normal.

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