When a scientist is killed, Dr. Rodney McKay believes poor circuitry is at fault. However, when another scientist is killed, Doctor McKay suspects foul play. McKay is then alerted to a Wraith-encoded virus which quickly takes control of the ship's computer, and the crew becomes increasingly powerless. The team races against the clock to keep their ship from turning against them.

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In their continuing search for the Wraith-infected Ford, the team encounters Ronon Dex, a fierce warrior who survived a battle with a Wraith and has been on the run ever since. Ronon reveals that he konws os Ford's whereabouts. Upon finding Lietenant Ford, the team quickly realises they may never be able to save Ford from what he has become.

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After being rescued from a Wraith Dart during a sudden attack, Doctor McKay and a new team member Lieutenant Laura Cadman are trapped inside the transport equipment when the Dart crashes. Dr. Zelenka's attempt to materialise McKay is successful, but McKay finds he has and unexpected guest in his own body: Cadman's consciousness has been extracted with him and is inside his head!

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Sheppard's team discovers a planet untouched by the Wraith as they send their criminals to a penal colony for the Wraith to feed upon and Sheppard's Jumper crashes on this island.

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Ronon Dex discovers that a small number of his people survived the Wraith attack on his planet, including his former military trainer, with whom he has unfinished business. Meanwhile, McKay puts Atlantis at risk when he tries to unlock the secrets of an Ancient power source.

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A synthetic virus created by Dr. Beckett to revert Wraith's to human form puts Sheppard's life in jeopardy after the team encounters a girl in the early stages of Wraith development.

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A mission goes wrong when Sheppard begins transforming into a Wraith after being attacked. The Atlantis team races against time to reverse the conversion.

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The team finds a large Ancient Ship called Aurora off-world and it still has Ancients living on board.

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Lieutenant Ford, who now has his own team of super-soldiers, asks for Colonel Sheppard's assistance in an attack on a Wraith Hive ship.

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McKay attempts to rescue Sheppard, Teyla and Ronon from the Wraith hive ship that Ford wanted to sabotage and destroy.

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Colonel Sheppard is separated from his team while investigating an Ancient device; he finds himself in a domain where time is dilated, progressing faster than normal. Doctor McKay frantically looks for a way to save Sheppard before time runs out!

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SGC discover that The Trust has placed a bomb in Atlantis that will go off when Atlantis dials Earth. Daedelus must warn Atlantis and the team must find the traitor in their midst.

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Dr. McKay is trapped underwater in a sinking Puddle Jumper and he must rely on Samantha Carter for his survival.

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The team discovers an exact replica of Atlantis on a planet they are exploring. The planet is protected by The Protector who uses the technology to keep the villagers in line and the Wraith away. The Protector is dying and Sheppard is caught up in a dispute among the heirs of the throne.

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Alien combatants look to settle an ancient score by using Weir and Sheppard as pawns.

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When the Atlantis team finds out that the Genii have grown into a new menace, they realize that the armistice with their old enemy may soon come to an end.

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A Lieutenant suspects that he is a Wraith turned human by Dr. Beckett's new drug.

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Dr. McKay must save the team when they are caught on a planet with a super-volcano and there is no visible way out.

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Atlantis joins forces with a Wraith faction led by Michael, the Wraith they tried to turn into a human, who seeks their help in destroying their common enemies.

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