2.01 "The Siege Part 3"
- As Lt. Aiden Ford recovers from his near-fatal encounter with a Wraith, the team races against time to save the city from an impending Wraith assault.
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2.02 "The Intruder"
- A mysterious intruder has infected the Daedalus's computers with a virus that may allow them to take control of the ship.
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2.03 "Runner"
- Ronon Dex, a fierce survivor of a Wraith attack, may be the team’s only hope in combating the now dangerous, Wraith-infected Ford.
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2.04 "Duet"
- A technical glitch during their rescue from a Wraith ship forces McKay and Lt. Cadman to coexist inside McKay's body.
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2.05 "Condemned"
- The team visits a technologically advanced planet inhabited by a civilization mysteriously unharmed by the Wraith.
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2.06 "Trinity"
- McKay may have found a new and potent source of energy for Atlantis based on un-perfected Ancient technology.
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2.07 "Instinct"
- While experimenting with a retrovirus that could turn Wraiths back into humans, Dr. Beckett inadvertently puts Sheppard's life at risk.
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2.08 "Conversion"
- The team races to find a cure for the retrovirus that is mutating Sheppard into a Wraith.
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2.09 "Aurora"
- The discovery of an Ancient warship whose millennia-old crew lives in a virtual environment leads Sheppard and his crew into a direct confrontation with the Wraith.
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2.10 "The Lost Boys Part 1"
- As they are exploring a new planet, Sheppard and his crew find Lt. Aidan Ford living in a cave under the influence of a powerful drug and planning revenge on the Wraith.
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2.11 "The Hive Part 2"
- The effects of the enzyme’s grip on the Atlantis team begin to wear off, sending them into withdrawal as they look to escape from the Wraith hive ship.
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2.12 "Epiphany"
- Sheppard is pulled through a mysterious portal and trapped in a world inhabited by Ancients who are terrorized by a large shadowy monster.
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2.13 "Critical Mass"
- The team races against time to foil the Goa'uld's plans to destroy Atlantis.
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2.14 "Grace Under Pressure"
- Help comes to McKay in an unlikely form after his puddle jumper crash-lands in the ocean.
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2.15 "The Tower"
- The team encounters a village with an enigmatic leader who possesses the ability to protect his subjects from Wraith attacks.
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2.16 "The Long Goodbye"
- Sheppard and Weir become a threat to Atlantis when their minds are taken over by hostile entities.
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2.17 "Coup D'Etat"
- When the team learns that the Genii are posing a new, dangerous threat, they realize that the truce with their old foe may be at an end.
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2.18 "Michael"
- When the team attempts to turn a Wraith into a human with Dr. Beckett's perfected vaccine, the results are disastrous.
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2.19 "Inferno"
- McKay must save the team when they are trapped on a planet with a super-volcano.
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2.20 "Allies Part 1"
- The team is shocked when the Wraith call for an alliance.
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