John Sheppard was an experienced and a talented US Air Force Officer in Afghanistan, though his reputation was somewhat tarnished when he disobeyed a direct order in an unsuccessful attempt to save the lives of several US servicemen. When called upon to transport Brigadier General Jack O'Neill to the research base that had been established at the nearby Ancient defense facility, he inadvertently discovered that he not only had the ATA gene (the genetic factor necessary to activate Ancient technology), but that he was naturally proficient at using it. After some doubts, he finally joined the expedition to Atlantis, although Colonel Marshall Sumner made it clear he was not pleased about Sheppard's involvement in the mission.