Major Leonard's team fails to check in with Atlantis while on a mission exploring an anomalous energy spike. Because the anomaly also makes radio transmission impossible Sheppard must assemble a team in search of the missing men. When the team arrives on the planet they're shocked to find the bodies of several Genii soldiers who have apparently killed each other.

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.