A new group of explorers travel to the distant Pegasus Galaxy, where it discovers the advanced but deserted city of Atlantis on the ocean floor. Stranded in a new galaxy, without the possiblitity of returning to Earth, the team encounters a group of nomadic humans and a deadly enemy that feeds on humans as an energy source!

A secret base built by the Ancients is found in the ice in Antarctica. The Stargate Atlantis team is sent on a one-way mission to explore the distant Pegasus galaxy. The team encounters many new civilizations, including the sinister Wraith.

Sparks fly when Woolsey becomes the new leader of the Atlantis team; McKay faces difficult personal challenges; Teyla must balance her roles as mother and warrior; Ronan's past returns with a vengeance; and Kelly finds peril, then help, from an unlikely source. A provisional relationship with the Wraith takes a shocking turn and new adversaries test the team's courage and resolve like never before.