Season synopsis
Contains spoilers for this season and earlier seasons.
Carter leads the rescue after Michael’s trap, and Teyla gives birth before Sheppard’s team brings her home. Richard Woolsey then takes command of Atlantis. Michael later returns to seize Teyla’s son for his hybrid program. The expedition retakes the city after his forces infiltrate it, and Teyla kills him during the fight. Elsewhere, the team tries to keep the Wraith from turning the human worlds into a supply line: Dr. Keller proposes gene therapy that could remove the need for feeding, while Todd's alliance shifts with each new danger and bargain.
A search for Ancient technology brings Daniel Jackson and McKay into conflict with a group of rogue Asgard and their Attero device, which can destroy Wraith ships in hyperspace but makes activated Stargates explode. The team stops the device and rescues its captives, then continues to manage the damage caused by its past interventions when a coalition of Pegasus worlds puts the expedition on trial. McKay and Keller begin a relationship, while Carson Beckett's clone returns from stasis to help Keller and later aids human survivors of the Hoffan plague; he remains distinct from the Carson who died in season three.
In “Ghost in the Machine,” Weir's consciousness returns in the FRAN Replicator template after the faction she joined fails to ascend. When one of them threatens Atlantis, Weir stops him and leads the others through a Stargate secretly connected to a Spacegate, knowingly leaving herself and the group stranded in space. The final Wraith threat comes from a super Hive ship powered by stolen Zero Point Modules. Atlantis uses its wormhole drive to reach Earth, Sheppard destroys the ship from within, and the city lands, cloaked, in the waters outside San Francisco.