Atlantis is back on earth and the IOA is now calling the shots. Not for long, however. A series of events leads the expedition back to the Pegasus Galaxy. After a hijacking, the city finds itself on a new planet, but this time the planet is inhabited by people who claim to be direct descendants of the Ancestors. McKay finds a treasure trove of new Ancient technology on the planet, and someone who was once lost returns.
In this season, the Wraith are still a huge threat. The Coalition demand for more cooperation. The Genii make themselves known again. New enemies and old ones try to thwart the Lanteans at every turn. Despite the further odds, old and new friends make a stand to help Atlantis in the new fight to re-establish themselves in the Pegasus Galaxy.