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- A team of scientists think they have found the location of the long lost city of Atlantis. It can be reached by a Stargate address that leads to the Pegasus galaxy.
- 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.
- It's Elizabeth's birthday and she gets a very special gift: a woman who has been in stasis in an Atlantis' laboratory for 10,000 years and is actually herself.
- Rodney investigates a ZPM from a planet whose inhabitants kill themselves when they turned 25 years old to prevent the Wraith from feeding on them.
- 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.
- Rodney can't remove an Ancient device that makes him invincible but prevents him from eating or drinking. Meanwhile, there are power malfunctions throughout the city and one of the Athosians mentions seeing a shadow.
- A strange energy generating fog allows travel back to Earth. But something's wrong.
- A team of scientists, including McKay, Zelenka and Ford, are exposed to a deadly virus. Sheppard goes after one of the scientists trying to escape.
- 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.
- McKay finds a way to send a message to Earth, leaving space for personal messages. Sheppard and Teyla are off to spy on the Wraith fleet approaching Atlantis.
- 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.
- Atlantis offers help to the Hoffans, who are working on a defense against 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.
- Sheppard invites a priestess, who claims to not know about a weapon protecting her planet from the Wraith, to Atlantis to discuss asylum for refugees.
- There's suspicion of a Wraith collaborator and some of the team suspect the Athosians. Ford and Sheppard find land on Atlantis' planet.
- The team is on Dagan, where they must find key stones to retrieve a ZPM. Zelenka finds out Atlantis has a deep space scanner.
- Major John Sheppard, Dr Rodney McKay and two other scientists explore a planet where a Wraith spaceship, which crashed there 10,000 years ago, during the Atlantis-Wraith War, is still sending an SOS signal.
- McKay and Weir start repairing the grounding station, while Sheppard tries to fight Kolya. The puddle jumper on the mainland enters the eye of the storm.