The Daedelus arrives in time to save Sheppard and destroy the attacking hive ships. But more are on their way. Ford is attacked by a Wraith, and gets a massive dose of Wraith enzyme, which changes him, making him strong and violent. He steals a puddle-jumper and flees through the gate. The crew convince the Wraith that they have destroyed Atlantis, by exploding a nuke, then cloaking the city. The Wraith retire.
The Atlantis command crew are on their way back from a visit to Earth, in the Daedelus, when it is struck by an intelligent Wraith virus. They must overcome it before it delivers the Daedelus, all its technology, and stargate codes, into Wraith hands, but it seems one step ahead of them all the time.
Exploring a new world, the team find a dead Wraith, with its enzyme sac cut out. So they start searching for Ford -- but Sheppard and Tayla get captured by a Runner, Ronon Dex -- a human implanted with a tracker that the Wraith can hunt. They miss capturing Ford, but remove the tracker device from Ronon. He then discovers that his home world has been laid waste by the Wraith.
On a routine patrol, McKay and Lt Cadman are transported into a Wraith Dart. The craft is captured, but there is a problem rematerialising them. McKay reappears, but with Cadman's consciousness also residing in his head. Ronon joins Sheppard's team.
The team arrive on on a planet that uses prisoners to feed the Wraith. By they get captured by those prisoners, who are determined to escape. Dr Weir arrives to help rescue them, and discovers that the "crimes" of the prisoners are becoming more and more trivial, in order to populate the prison island. Then the Wraith arrive.
The team find some powerful Ancient weapons. McKay thinks he knows how to fix them, but he is overconfident, and nearly kills everyone.
The team find a planet with a wild Wraith in the woods, terrorising a village. When they go to kill it, they find a young female Wraith who has been raised as human, by a man who says he has found a potion that stops the hunger. However, it hasn't been working, and the girl has been feeding. Dr Backett is excited that they can try out the retro-virus that could make the Wraith human. But the girl injects herself with unproven virus, and transforms more fully into a Wraith. The team are forced to kill her.
Sheppard has been infected with the retro-virus via the Wraith wound, and starts to convert into a bug-like creature. The race is on to find an anti-viral to cure him.
The team and the Daedelus go to investigate the Aurora , an Ancient spaceship on the other side of the Pegasus Galaxy. They find the crew in stasis, their minds exercised in a VR. Sheppard goes in to contact them, and discovers they don't know it's a VR, and they they are trying to get back to Atlantis to deliver a communique on a fatal Wraith weakness. Meanwhile the rest of the team discover on of the crew has been replaced by a Wraith, who is trying to discover the secrets of intergalactic hyperdrive. And two Wraith cruisers are on their way.
Lt Ford has gathered a gang of Wraith enzyme-enhanced followers. They kidnap the team, and infect Tayla and Ronon with the enzyme, to prove it is not harmful. They also plan an attack on a Wraith Hive ship, with only McKay left behind as a hostage for the others' good behaviour. But things go wrong, and they are captured by the Wraith...
Sheppard and the rest escape, but get recaptured whilst rescuing a prisoner. One of Ford's men dies from enzyme withdrawal. McKay escapes by injecting himself with a massive dose of the enzyme, then has to undergo cold turkey to recover. He tells the Daedelus where the Hive ships are. The team escape, and Sheppard manages to get the Hive ships to fight and destroy each other. The Daedelus witnesses the destruction, and assume the team is dead -- but they made it down to the planet and back to Atlantis through its Stargate.
Sheppard gets trapped in an Ancient time dilation field, where time runs much faster. The crew rush to save him before he dies of old age. Meanwhile, he meets a group of people meditating their way to ascension, stopped only by a fearsome Beast.
The Goa'uld have planted a bomb in Atlantis. The race is on to find the Goa'uld agent to get the access codes to stop the city being destroyed. Weir authorises the extraction the information from her prime suspect by force. But then the Goa'uld turns up in a very unexpected place.
McKay is trapped a thousand feet under water in a crashed puddle jumper. As his power runs out, and the cabin slowly floods, he hallucinates Sam Carter as a source of advice.
The team find a pastoral society protected from the Wraith, and exploited, by a ruling class who live in a place that looks similar to Atlantis. When they discover that Sheppard has the Ancient gene, he is "invited" to the city. But machinations are under way to replace the current ruler. McKay manages to drain the city's ZPM, thus discrediting the rulers who can no longer control the city. They discover this city has a good supply of drone missiles, and restock.
Dr Weir is taken over temporarily by a dying woman, who asks a last favour -- that Sheppard host her dying husband for a final goodbye. But they are actually implacable enemies, and, with access to their hosts memories and access codes, they put Atlantis in grave danger trying to kill each other.
An away team are apparently killed and burned by peaceful villagers - Tayla and Ronan are sent to discover why. Meanwhile a renegade Genii offers Atlantis a ZPM in exchange for enough weapons to mount a coup. Atlantis instead warn the Genii and mount an attack to steal back the ZPM. But the ZPM is out of power: it is all a ploy to capture Sheppard and his team, and the original away team, as hostages in exchange for 10 puddlejumpers. But the pretend renegade turns real renegade when he learns Atlantis can cure his sister of radiation sickness, and frees the hostages.
Carson has tried out his experimental retrovirus on a captured Wraith, who has become "human" but amnesiac. The Atlantis crew tell him he is an injured team-mate, Michael. When he discovers the truth, he feels betrayed, turns violent, and escapes back to the Wraith. Now the secret of the survival of Atlantis is out in the open.
Atlantis answers a distress call from a planet who are having problems with their Ancient shield. McKay discovers the whole installation is on top of a supervolcano that is about to blow. The colony has to be evacuated. The colony also has an Aurora-class ship, but they don't know how to work it. McKay manages to fix it just in time to evacuate the final refugees. The grateful colony loan the ship to Atlantis -- which is just as well, as they've spotted a Wraith Hive ship, three weeks out...
The Wraith ship contacts Atlantis. Michael explains that there is civil war amongst the Wraith because of poor feeding grounds, and offers a deal -- give them the retrovirus, so they can turn other Wraith ships into food. But it's a trick -- they sneak a virus into Atlantis that gives them the location of Earth...