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.

Colonel Samantha Carter takes charge as the city's new leader, facing new and daunting challenges, including joining forces with the dangerous Wraith in order to fight a common enemy-- the seemingly unstoppable Replicators.

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.