After narrowly surviving a massive Wraith attack, the new inhabitants of Atlantis continue to uncover the secrets of the ancients and search for allies in their corner of the universe, but the persistant threat of interference from vicious enemies haunt them in their pursuits. Will they find the elusive power source they so desperately need or the renegade team member they've lost?

A fleet of Wraith ships races to attack Earth. Can the team stop them in time, or do the Wraith have a new feeding ground? Will a technologically advanced people prove to be allies with the Atlantis expedition, or will they be a powerful new threat?

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.