The Daedalus arrives and the two hive ships are destroyed. Atlantis seems saved, then Zelenka detects 12 more ships. Ford seems changed after a fall in the water.
McKay, Sheppard, Beckett and Weir are on the Daedalus. McKay finds a Wraith virus that is infecting ship systems and sending a signal to the Wraith.
The team is searching for Ford on a planet. Teyla and Sheppard are taken hostage by a stranger, while Ford tries to convince McKay that he's normal.
After an attempt to retrieve McKay and soldier Laura Cadman from the memory banks of a Wraith dart, Cadman gets stuck in McKay's mind.
The team discovers a planet where the stargate is kept on a prison island to keep the Wraith satisfied. Their magistrate is willing to trade a rare mineral.
The team discover an Ancient project to create the ultimate power source. McKay thinks he can finish it. Ronon finds out he is not the only surviving Satedan.
The team find a hidden Wraith girl, cared for by a man with a serum stilling her hunger. Beckett wants to perfect a retrovirus turning Wraith into Humans.
Sheppard is infected with the Wraith retrovirus and slowly turns into an Iratus bug. To provide a treatment stem cells must be retrieved from one of their eggs.
McKay finds an Ancient warship adrift in space. Sheppard finds out they are carrying a communique that mentions a weakness in Wraith technology.
The team is captured by Ford and are forced to take the Wraith enzyme. Ford has a plan.
Sheppard's interrogation is suddenly aborted. Teyla senses another hive ship has arrived. Meanwhile McKay tries to convince his guard to call in help
The teams discovers a ridge that can only be entered through a door. Sheppard gets pulled in by a field. McKay discovers time goes very fast behind it.
The Trust, a Goa'uld terrorist organization, has planted a bomb in Atlantis.
McKay and a pilot crash with a puddle jumper into the ocean on Atlantis. They start to sink.
The Stargate Atlantis team finds a world where the leader lives in a tower who possesses the power to stop the Wraith attacks.
The team discovers two life pods with a dying woman and man in it. Upon opening Weir gets imprinted with the mind of the woman. She asks a special favor.
While Teyla and Ronon investigate the mysterious death of major Lorne, the Genii Ladon Radim contacts Atlantis. He wants to trade in a ZPM.
Michael Kenmore, a new lieutenant, awakes in the infirmary and doesn't remember a thing. The crew is very concerned about his well-being, he seems different.
Atlantis helps with repairing an Ancient shield generator on Taranis. They discover the Taranians are in possession of an Ancient warship.
The hive ship approaching Atlantis is Michael's. He wants a trade: the retrovirus for not revealing the secret of Atlantis and insights on Wraith technology.
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