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.