status of the Atlantis expedition. General Hank Landry implied to Weir that the Pentagon wanted to make Colonel Steven Caldwell the military commander of the Atlantis expedition, but Weir informed them that Atlantis already had a military commander. When they stated that Sheppard was just a major with a questionable record, she told them that they could solve that problem with the President and the International Oversight Committee on her side; Sheppard was subsequently promoted to the rank of lieutenant colonel and installed as official military commander of the Atlantis expedition. Colonel Caldwell, who had sought the leadership position, was displeased by this outcome. 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. After piloting Atlantis to a new home, Sheppard fell under the command of Colonel Samantha Carter, the new leader of Atlantis. He acted as her second-in-command during the war with the Replicators, a war which reunited him with the Wraith he later named "Todd." Thanks to a brilliant plan by McKay, the Replicators were destroyed by an alliance of Wraith and human forces, but a new threat emerged in the form of the former Wraith, Michael, who kidnapped Teyla. After rescuing Teyla and apparently killing Michael, Sheppard encountered a new change of command as Richard Woolsey took over Atlantis. Under Woolsey, Sheppard continued to lead efforts to fight the Wraith and Michael, who returned a final time to takeover Atlantis. With the help of Todd, Sheppard and his team attempted to find a way