 John Sheppard played by Joe Flanigan is a USAF Lieutenant Colonel (ranked major in season 1).He is an experienced and a talented US Air Force Officer in Afghanistan, though his reputation is 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 into the research base that has been established at the nearby Ancient defense facility, Sheppard inadvertently discovers that he not only has the ATA gene (the genetic factor necessary to activate Ancient technology), but that he is naturally proficient at using it.