 After some doubts, he finally joins the expedition to Atlantis, although Colonel Marshall Sumner makes it clear he is not pleased about Sheppard's involvement in the mission.In Season 1, Sheppard serves as both a Major and later also becomes the military commander following Colonel Sumner's death.In Season 2, Sheppard is eventually promoted to Lieutenant Colonel and still remains as Atlantis's military commander with Sheppard serving as the team leader for the Atlantis Expedition's team, the First Atlantis Reconnaissance Team or AR-1.