When a massive storm threatens the city, Atlantis is evacuated -- only to be taken over by the team's newest enemy.

Major Sheppard plays a dangerous game of cat and mouse with soldiers who have seized control of Atlantis and have taken Weir and McKay hostage.

The team searches for a valuable Zero Point Module rumored to be hidden on the planet Dagan -- but their new allies have motives of their own.

While being evaluated by the International Oversight Advisory, Richard Woolsey meets a beautiful scientist new to Atlantis, who is not what she appears. Meanwhile, Lt. Colonel John Sheppard is captured and tortured by an enemy he thought he'd killed several years ago: his sworn enemy, Genii Commander Acastus Kolya.