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- Season 2 overviewJul 15, 2005-Mar 10, 200620 episodesSeason 2 episodes1. The Siege Jul 15, 2005
- Ford recovers from his encounter with the Wraith; the team races to save the city from an assault.
- 2. The Intruder Jul 22, 2005
- McKay fears that a computer virus on Col. Caldwell's ship might be the work of the Wraith.
- 3. Runner Jul 29, 2005
- A fierce survivor of a Wraith attack must help the team combat the dangerous, infected Ford.
- 4. Duet Aug 5, 2005
- A glitch forces McKay and Lt. Cadman to coexist inside McKay's body.
- 5. Condemned Aug 12, 2005
- The team visits a technologically advanced planet that is mysteriously unharmed by the Wraith.
- 6. Trinity Aug 19, 2005
- Unperfected ancient technology could become the new source of energy for Atlantis.
- 7. Instinct Aug 26, 2005
- Dr. Beckett inadvertently puts Sheppard's life at risk while experimenting with a retrovirus.
- 8. Conversion Sep 9, 2005
- The team races to find a cure for the retrovirus that is mutating Sheppard into a Wraith.
- 9. Aurora Sep 23, 2005
- The crew aboard an ancient ship has information about a weakness in the Wraith's technology.
- 10. The Lost Boys Sep 23, 2005
- Exploring a new planet, Sheppard and his crew find Ford living in a cave.
- 11. The Hive Jan 6, 2006
- McKay must rescue Sheppard, Teyla and Ronon from a hive ship.
- 12. Epiphany Jan 13, 2006
- Sheppard goes through a portal and cannot find his way back to Atlantis.
- 13. Critical Mass Jan 20, 2006
- The team races against time to foil the Goa'uld's plans to destroy Atlantis.
- 14. Grace Under Pressure Jan 27, 2006
- McKay receives help from an unlikely source after his puddle jumper crashes into the ocean.
- 15. The Tower Feb 3, 2006
- The team finds a village whose leader has the ability to protect his subjects from Wraith attacks.
- 16. The Long Goodbye Feb 10, 2006
- Sheppard and Weir become a threat to Atlantis when hostile entities take over their minds.
- 17. Coup D'Etat Feb 17, 2006
- The team worries that their truce with the Genii might come to an end.
- 18. Michael Feb 24, 2006
- The team tries to turn a Wraith into a human using Dr. Beckett's vaccine.
- 19. Inferno Mar 3, 2006
- McKay must save the team when its members are trapped on a planet with a super volcano.
- 20. Allies Mar 10, 2006
- A Wraith offers a deal: Beckett's retrovirus in return for information about Wraith weapons.