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1-21 of 21
- An estranged father and son are re-united at a wedding party. However, a thunderstorm traps them in a cabin, forcing the family to reveal deeper secrets.
- 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.
- 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 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.
- 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.
- While Teyla and Ronon investigate the apparent death of Major Lorne, the Genii Ladon Radim contacts Atlantis. He wants to trade a ZPM for weapons supplies.
- The Trust, a Goa'uld terrorist organization, has planted a bomb in Atlantis.
- After an attempt to retrieve McKay and Lt. Laura Cadman from the memory banks of a Wraith dart, Cadman gets stuck in McKay's mind.
- 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.
- McKay and a pilot crash with a puddle jumper into the ocean on Atlantis. They start to sink.
- The team find a hidden Wraith girl, cared for by a man with a serum that he claims can satisfy her hunger. Beckett wants to perfect a retrovirus that can turn Wraith into humans.
- Michael Kenmore, a new lieutenant, awakes in the infirmary and doesn't remember a thing. The other expedition members are very concerned about his well-being as he seems different.
- 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.
- Sheppard's interrogation is suddenly aborted. Teyla senses another hive ship has arrived. Meanwhile McKay tries to convince his guard to call in help.
- 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 discovers two life pods with a dying woman and man in them. When they are opened, Weir gets imprinted with the mind of the woman. She asks a special favor.
- The team is captured by Ford and are forced to take the Wraith enzyme. Ford has a plan.
- 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.
- Colonel Sheppard's team finds a world where the leader lives in a tower that possesses the power to stop Wraith attacks.
- 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.
- Atlantis helps with repairing an Ancient shield generator on Taranis. They discover the Taranians are in possession of an Ancient warship.