The Wraith have captured many of the Athosians and SGA expedition members, before leaving through the Stargate. Back at Atlantis the shields continue to lose power, due to the limited energy left in the last remaining ZPM. Major Sheppard eventually gets approval to lead a rescue mission to the Wraith’s ship’s location. The rescue team finds almost all the Wraith are in hibernation in the ship and the captured people stored in cocoons or holding cells.

Sheppard must find away to rescue the people, before more Wraith awaken, but he also is faced with making a terrible sacrifice along the way.