Atlantis has fallen out of hyperspace, and is adrift. Elizabeth Weir is in sickbay, dying from her injuries. The power conduits need to be repaired before they can get back into hyperspace, but power is leaking away at an alarming rate, and they have only hours to repair the station before too much power has been lost. Apollo has contacted Carter at Midway station, saying that they have lost Atlantis, and she is trying to figure out a way to find them. Several minor crises occur, and are averted, and the station is repaired, but too late to re-enter hyperspace. McKay saves Weir by reactivating her nanites; no-one is pleased with him. He then suggests using an experimental hyper-capable Jumper to raid the Replicator planet for spare ZPMs...
Sheppard, Ronan, McKay and Weir go to the Replicator planet to steal a ZPM. Rodney reactivates Weir's nanites, allowing her to guide the team through the Replicator city. They get the ZPM, and Rodney discovers a disabled command imperative to attack the Wraith. They decide to re-enable it, but this leads to Weir getting captured. She manages to take control of the Replicators long enough for the rest to escape, but they have to leave her behind. Meanwhile Carter and the Apollo find Atlantis. With the new ZPM it has enough power to find a new planet. Rodney detects the Replicators launching a massive attack fleet, against the Wraith.
Colonel Samantha Carter is put in charge of Atlantis. Ronan finds a group of his old friends, now famous Wraith hunters, and asks to bring them to Atlantis. Sam refuses, because of new standing orders to protect its location. Sam also refuses to let Sheppard try to rescue Dr Weir. Ronan begins to question whether his loyalties are with his old comrades, or with Atlantis. The old friends persuade the team to attack a Wraith scientific base, where they are trying to break the Replicator attack program. But it's a trap. Ronan ends up having to kill two of his old companions, and stays in Atlantis.
Sheppard is compelled to touch a strange crystal on a dark planet. He seems fine, but then people who come into contact with him start having nightmares about him. It seems there is an alien entity feeding off their fear. It is isolated in MacKay, and Sheppard has to enter his subconscious to help him evict it.
Sheppard is captured by a bunch of humans who have been perpetually travelling for thousands of years, but are now running out of ships. They have found an Ancient ship, and need his help start it. But they try to get this by kidnapping and torture, so he is not inclinded to help. A series of fortune reversls ensue, along with a fight with the Wraith. Eventually, they form an Alliance and Sheppard is freed.
A mutated bacterium infects everyone on Atlantis, except Teyla and Ronan, who are immune to the childhood variant. The illness causes progressive amnesia, and it is difficult to find a cure when no-one can remember what they are supposed to be doing.
Teyla and Dr. Keller go to visit Tayla's Athosian people, but find them all missing and themselves in mortal danger fromthe Bola Kai, a group of primitive warriors. Keller is a self confessed "wimp", and has difficulty keeping up with Teyla as they have to run and hide through the woods. They find a wounded man, who claims he is a Genii spy who saw the Athosians harvested by the Wraith. They are captured by the Bola Kai, who deny being Wraith-worshipes, and demand the gate address of their home. Keller lies, to buy time. Then the Genii frees them, but turns on them, knocking out Teyla, and demanding the gate address of Atlantis from Keller. He is the one who betrayed Teyla's people, and Keller saves Teyla's life by shooting him, in the leg. He escapes, and they are rescued by their teammates. In the infirmary, Keller says she has to speak to Teyla about her medical test results...
Teyla hears of a seer who might be able to help her find her people. She locates him, but he is dying. He shows Rodney a vision of the team being ambushed by Wraith. Later, a Wraith contacts them, asking for help in defeating the Replicators, who are now destroying the Wraiths' food supply -- human colonies. The seer shows scenes of destruction of Atlantis to Carter, and of a Wraith ship to Teyla, before he dies. The Wraith arrive at Atlantis to work on the Replicator virus, but another Wraith ship arrives. They fight and destroy each other, as in Teyla's vision. The vision of Atlantis being destroyed is yet to come...
McKay is working on the Replicator virus, and emails his sister Jeanie Miller for help. She is kidnapped, and the team go to earth to find her. Then Rodney is kidnapped, too. The head of a medical company working on alien technology needs their help to save his daughter, dying of leukaemia, who he has infected with nanites to cure her, but they aren't working. He infects Jeanie with the same nanites, to give them an incentive to work on the cure. They manage to get the nanites to work and cure the daughter's cancer, but then they won't switch off, and continue to try to cure her further, in the end killing her. There is a desperate race to save Jeanie before they kill her too, and Rodney has to ask the Wraith prisoner to help. But he needs to feed...
The team notice people behaving strangely in Atlantis. Then they discover that they heal immediately. Further investigations show they are full of nanites, and all the other personnel are Replicators. Then they discover Elizabeth Weir. The Replicators tell them all that they have been manufactured by the nanites, with memories downloaded from the last time the real team, and that the real Weir died several months ago. These breakaway group of Replicators want to study them to understand how to ascend. Then the main Replicators discover the fake city and destroy it (bring the Seer's vision true), and the five escape, with a device that can track Replicator ships. They contact the real Atlantis team and given them the device. The Replicators catch up with them, and the manufactured team create a diversion, allowing the real team to escape. McKay uses the device, and discovers there are a lot of Replicator ships.
Sheppard discovers that Teyla is pregnant, and removes her from active duty. Atlantis, the Wraith, and the Travellers cooperate to destroy the Replicators' home world. At the end, we see a spaceship drifting through the fragments of the destroyed planet, captained by a black clad, grimly smiling ... Elizabeth Weir.
The Wraith working with Atlantis liberated some ZPMs from the Replicator home world before it was destroyed, and are now attempting to build an enormous Wraith clone army, to gain ascendancy over the other Wraith. However, he is betrayed by one of his crew, and captured. But first he sends a distress call. The Atlantis team follow it, discover the plot, and destroy the clone factory.
A freak ion storm activates Atlantis' quarantine shutdown, locking all doors, and isolating people all over the city. McKay is locked in the botany room with his girlfriend, but no access to a computer. Carter and Zelenka are trapped in a lift, with only a laptop. Ronan and Dr Keller are trapped in the infirmary. And Sheppard and Teyla are trapped in the lab. They all battle to regain control of the city, but then they discover it is emitting an emergency beacon to all space...
Sheppard and McKay are forced to escort a bratty princess, Harmony, to her proving ground in the forest. On the way, they are attacked by Genii, who want to kill Harmony so that her sister will become queen, and resume trading with them. Eventually they come to the meditation place -- Ancient technology that controls the "beast" in the forest.
A strange woman accosts Sheppard at his father's funeral -- she says a scientist has created a replicator robot who has killed and escaped. They track down the robot, only to discover that the woman is one as well when she comes to their rescue.
Carter, Keller and McKay are trapped in an underground cavern on a planet rocked by tremors.
Teal'c comes to Atlantis to coach Ronan on passin his IOA interview, but Ronan is hostile. On their way back to earth, they stop off at the Midway station, when it is overrun by Wraith, who move on to SGC. Ronan and Teal'c pursue, and bond while beating the Wraith.
Teyla has visions from Kanaan, the father of her child, telling to search for him and the rest of her people [ 4.07 Missing ] . Meanwhile, Dr Keller reports on a plague that is affecting several random planets, with a 30% death toll: it is a variant of the Hoffan virus [ 1.07 Poisoning the Well ] . Teyla travels to the planet Kanaan told her of, but it is a trap, and she is abducted by the Wraith-hybrid Michael, who is turning her people into a superarmy to destroy the Wraith. The "friendly" Wraith Todd offers to help Atlantis in exchange for the secret of the virus, which he intends to use against other Wraith. The team use Todd's information to track Teyla, but instead, find Dr Carson Beckett...
They discover that Carson is a clone made by Michael. He helps them try to track down Teyla, but they keep just missing her. They do rescue the remaining Athosians, however. Michael wants Teyla's baby, the child of two humans with the "gift" of Wraith DNA, for his own purposes. Clone Carson is aging rapidly without his Wraith medicine, and is put in stasis until a cure can be found...
Returning from a failed search for Teyla, Sheppard steps through the gate to a deserted Altantis. A holographic old McKay appears, telling him a glitch has sent him 48000 years into the future -- a future where Michael's plans for Pegasus domination succeeded. McKay has a plan to return Sheppard and change the timeline, by telling him where to find Teyla. Sheppard returns, the team goes to the place, but it is boobytrapped, and the whole building implodes...