Season synopsis
Contains spoilers for this season and earlier seasons.
Atlantis begins the season adrift after the Asuran satellite attack, with its shield and power failing and Weir critically injured. McKay and Keller reactivate dormant Replicator nanites to save her, and Sheppard leads a risky mission to steal a Zero Point Module from the Asuran homeworld. Weir uses her connection to the Replicator network to help the team alter the Asurans' attack code, then stays behind when Oberoth's forces close in. The others escape with the ZPM and move Atlantis to a new ocean world; they believe Weir has been lost.
Colonel Samantha Carter arrives to lead the expedition as the Asurans turn their war on the Wraith and begin attacking the human worlds the Wraith depend on. The team forms a wary alliance with Todd, a Wraith prisoner who knows the Asurans' plan, and eventually gathers Wraith and Traveler ships for a battle against the Replicator homeworld. Their plan destroys that city and its collective, but the ending shows Weir commanding a surviving Replicator ship, leaving the expedition unaware that her story continues.
Michael kidnaps the pregnant Teyla and uses Athosian prisoners in his hybrid experiments. The team frees the Athosians but cannot stop him escaping with her. They also recover a clone of Beckett, created from stolen DNA; Keller places him in stasis when his condition deteriorates. Searching for Teyla, Sheppard is thrown 48,000 years into a ruined future. A McKay hologram helps him return to the present with her location, but his rescue team reaches Michael’s base too early and triggers a trap. The building collapses around them as the season ends.