Stargate Atlantis: Season 3, Episode 11

3 - 11: The Return, Part 2

General O'Neill and Richard Woolsey, the lone survivors of the replicators' bloody coup of Atlantis, hide out in an abandoned section of the city. Knowing O'Neil gave General Landry a standing order to nuke Atlantis if a foothold situation should ever arise, the two lay low awaiting their fate.