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7/11/08Colonel Carter attempts to lead a rescue mission to save several trapped Atlantis team members, unaware that Michael is closing in on their position with a heavy cruiser.
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7/18/08After Dr. Keller removes Beckett from stasis, she gets infected with a dangerous entity that begins taking over Atlantis.
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7/25/08Ronon is captured by his former friend Tyre, who plans to turn him over to the Wraith to get back in their good graces.
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8/1/08Sheppard's team finds the Earth ship Daedalus abandoned and without power.
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8/15/08When Sheppard and his team are about to return from an off world mission with their Puddle Jumper, the systems of the Jumper go crazy. Barely able to return to Atlantis, the Jumper seems to infect the city's systems with what seems to be a computer virus.
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8/22/08McKay begins to lose his memory after contracting the Pegasus version of Alzheimer's called "Second Childhood."
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9/5/08Sheppard and Beckett are terrorized by deadly creatures on a planet housing one of Michael's research facilities.
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9/12/08Sheppard's team accompanies Todd the Wraith on a mission to negotiate an alliance with another Hive with Teyla playing a key role when she's surgically altered to be a Wraith Queen.
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9/19/08Keller is abducted on a trip off world to help a wraith-threatened village, and it's up to Ronon and McKay to find her. However it soon emerges that her abductor is, in fact, a Runner.
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9/26/08Daniel Jackson visits Atlantis to do some research on the Ancient scientist Janus.
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10/10/08Sheppard must rescue McKay and Daniel Jackson from an Ancient laboratory that belonged to Janus before Todd, who has hijacked the Daedalus, gets there first.
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10/17/08When the Wraith discover that a small group of survivors of Michael's release of the modified Hoffan drug are hiding among the population of a village on another planet, Sheppard and his team must convince the entire village to evacuate before a Hive Ship arrives.
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10/24/08When Sheppard and his team are brought to trial by a Coalition of human worlds for what they claim are crimes against the people of the galaxy, it's up to Woolsey's legal expertise to clear their names.
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11/7/08Michael besieges Atlantis in an attempt to kidnap Teyla's infant child.
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11/14/08While exploring the mainland of Atlantis' planet, Sheppard is captured by a foe believed to be long dead. Meanwhile, Woolsey's job is at risk and he has an important decision to make and McKay and Zelenka make an interesting undersea discovery.
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11/21/08McKay returns to Earth to witness the unveiling of his rival's latest breakthrough.
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12/5/08When a Wraith Hive Ship arrives in orbit above Atlantis and sends a distress message, Sheppard takes a team to investigate and discovers that the Wraith have been infected with a strange disease.
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12/12/08A thief uses an Ancient transfer device to switch her consciousness with Dr. Keller. While she attempts to escape Atlantis, Dr. Keller must deal with the thief's accomplices and angry villagers on her trail.
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1/2/09Detective John Sheppard investigates a series of unusual murders in Las Vegas.
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1/9/09Todd informs Atlantis that a rogue Wraith has acquired several Z.P.M.'s to power a formidable new Hive ship. When the Daedalus engages it in battle but is unable to defeat it, the team gets a message indicating it is headed to Earth.
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