Two Wraith hive ships are on their way to Earth, having captured McKay and Ronon, and with Sheppard sneaking along in pursuit. Atlantis are desperate to stop them, so Weir orders the Daedalus and Orion in pursuit, despite them being damaged. Ronon and McKay escape. Michael is shunned by the Wraith, and so defects to the human side, rescuing Sheppard. Daedalus and Orion arrive, destroy one Wraith ship, and disable the other, with Orion also being destroyed and Daedalus disabled. Sheppard, Ronon, McKay and Michael go to Daedalus, and decide to use the retrovirus on the remaining Wraith ship, which they then capture. Meanwhile, Weir is called back to Earth to answer to IOA for her actions...
Sheppard and his team fly the captured Wraith ship back to Atlantis, complete with 200-Wraith-turned-Human who they can't trust not to revert. So they take them to a secure planetary camp where they can be monitored and given their daily drug to keep them human. They forcibly drug Michael, too. However, in the camp some of the detainees begin to suspect, and to revert. They take over, capturing Dr Beckett, and call to a Wraith hive ship. The team manage to rescue Beckett, and blast the camp from orbit, before they are attacked by the arriving Wraith ship. Shielded, they await the arrival of the Daedalus. Meanwhile, IOA decide Weir can stay in charge of Atlantis, for now.
The team are searching for stargates to use as a bridge between the Pegasus galaxy and home. They find a settlement where one man, Lucius Lavin, seems to be held in surprisingly high esteem by all. He offers to trade medicines, and soon Dr Beckett falls under his spell, and brings him back to Atlantis. There, everyone becomes his friend, except Sheppard, who has a bad cold. Lucius [Harry Mudd by any other name...] is using a pheromone to make people like him, and Sheppard needs to get Dr Beckett to find an antidote.
Ronon is captured by some villagers, who accuse his of having brought the Wraith down on them when he was a runner. They hand him over to the Wraith, in return for a guarantee of immunity from further cullings, but are destroyed instead. The Wraith implant another tracking device in Ronan, and return him to his devastated home planet, and start hunting him again. Big mistake, as he goes all Rambo on them. Then his Atlantis team track him down, and help him kill the hunting Wraith.
Weir and the team discover another Atlantean-city, populated by what appear to be the descendants of the Ancients. However, in reality they are nano-constructs, Ancient weapons that went wrong, determined to wreak revenge on Atlantis.
Dr Weir wakes up in a mental institution, and is told the last two years are an hallucination brought on by a mental breakdown. However, in reality she is still on Atlantis, infected by nanites that need to get her to give up so that they can take over her body.
Sheppard is captured by a renegade Genii [2.17 Coup D'Etat], who demands Weir exchange the Genii leader for him, else he will be slowly killed by having a captive Wraith feed on him. She refuses. Sheppard and the Wraith team up and escape. The Wraith has fed on Sheppard enough to age him, but at the end returns that life to him. The Atlantis team arrives to help in the rescue, and Sheppard keeps his word in letting the Wraith go.
McKay's estranged sister publishes a maths paper that may result in harnessing unlimited energy from parallel universes. She is persuaded to go to Atlantis and work with McKay. They build a device that seems to work, but then it goes unstable. When they switch it off, an alternate-universe nice McKay appears, and tells them the machine is destroying his universe. In order to shut it down safely, and send other-McKay back, they end up depleting their ZPM.
Sheppard and his team go after another team who have failed to return from exploring an uninhabited planet. They discover piles of bodies: month-old dead Geneii, long gone dead Wraith, then the recently dead team. They all appeared to have killed each other. The one surviving member blows up the DHD, standing them all. McKay finds some damaged Wraith technology that is giving off a modulated low frequency emission. It appears to be messing with their minds. McKay must figure out how to switch it off before they all kill each other, too.
The Atlanteans discover an Ancient ship halfway between the Pegasus and Home galaxies. The Ancient survivors are grateful for their rescue, but demand that all the Earth residents return home. They are all trying to make a new life for themselves when they are recalled: Atlantis is under attack by Replicators, who have rewritten their base code that prevents them from attacking their creators.
Weir, Sheppard, and the team disobey orders to take Atlantis back from the Replicators (who have conveniently killed all the Ancients, solving that part of the problem).
A large group of whale-like creatures converge on Atlantis, and their sounds make people ill. Meanwhile Teyla, then others, start seeing images of Ancients trying to communicate. They discover these are linked: the whales are trying to warn them of an impending massive solar flare.
The team track down a heroic warrior, only to discover that it is Lucius Lavin [3.03 Irresistible], this time fooling people with a personal sheild. He saved the village from raiders in the past, but their gratitude is cooling, so he hires some ex-Genii mercenaries to pretend to raid the village, so that he can save them again. But real Genii turn up, searching for Sheppard. Sheppard convinces Lavin to lend him the sheild so that he can rescue the rest of his team. He manages this, killing the leader of the Genii, but the shield is depleted. He returns the sheild to Lavin without telling him this.
Rodney gets zapped by an Ancient device that is an Ascension Machine -- it increases his powers and intelligence, but unless he can reach the mental state of ascension too, he will die. [A sort of Flowers for Algernon, if you are an Anceint.]
Sheppard and MacKay have been playing an Ancient game of "Civilisation" for a couple of years. Only now they discover it isn't a simulation, it's real, and their two countries are on the brink of war due to their interference. The resolution is to get them to realise the horrors of war [a bit like the ST:ToS episode "A Taste of Armageddon"].
The team discover an old asteroid hollowed out and filled with technology. When Rodney powers it all up, a person appears from Wraith stasis. The asteroid contains the remnants of their civilisation, hiding from the Wraith. A second restoree admits that only half the people fleeing got away: some that were lost include the first man's family. In despair, he commits suicide, damaging the asteroid, that gradually moves into a decaying orbit [the celestial mechanics of this are more plausible than many such events, but I'm not convinced about he timescales]. The team want to abandon the asteroid, but the second restoree forces them to try to save the remaining population in stasis by abducting Tayla.
Many people are taking a day off, when a strange explosion rips through Atlantis. MacKay discovers that two of his staff exposed to Ancient radiation have become walking bombs, and one has exploded. The other is injured, being operated on by Dr Beckett...
The team are exploring an Ancient underwater mining operation, when they are joined by a Wraith queen. She wants to steal the puddlejumper to escape being trapped underwater, and has set the self-destruct on her own ship. But the puddlejumper gets flooded trapping them all on the sea floor. Tayla must somehow get the command code for the self-destruct from the Queen's mind.
The team find themselves stranded on a planet at the mercy of a horde of bug-wraith, engineered as killing machines by the Wraith Michael. Michael escapes, and they discover he has several other planets of bugs, ready to wreak his vengeance on Atlantis.
The Replicator planet is found to be building ships, possibly for an attack on Earth. So, against the advice of Dr Weir, Earth launches a "surgical first strike". The Replicators retaliate by attacking Atlantis. Their only defence is to leave the planet ("Cities in Flight"!). But in doing so, they sustain damage, Weir is badly injured, and Atlantis is left drifting lost in space, with only 24 hours of power left...