While testing a new "Gate bridge" that McKay and Lt. Colonel Samantha Carter created to accelerate transportation between Pegasus and the Milky Way, an Ancient ship was located, filled with living Ancients who reclaimed Atlantis. With the expedition disbanded, Sheppard was assigned command of an SG team. When General O'Neill sent a message to Stargate Command telling them that the Asurans had taken control of Atlantis, Sheppard, Weir, McKay, and Beckett hijacked a puddle jumper and traveled back to the Pegasus via the Gate Bridge. They tracked down Emmagan and Dex; the newly reunited team succeeded in rescuing O'Neill and Richard Woolsey and retook Atlantis. In the episode Adrift, Sheppard was forced to take command of Atlantis, since Weir was in a coma due to injuries that she sustained after Atlantis was grazed by the Replicator's beam. Sheppard later lost Weir during a mission to the Replicator homeworld in a successful effort to save Atlantis and turn the Replicators against the Wraith.