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John Sheppard is a fictional character in the Canadian-American military science fiction television series Stargate Atlantis, a science fiction show about a military team exploring the galaxy via a network of alien transportation devices. Portrayed by Joe Flanigan, Sheppard holds the military rank of Lieutenant Colonel in the series and is the second-in-command of the Atlantis Expedition after the death of Marshall Sumner (Robert Patrick) in "Rising".

Sheppard and Rodney McKay (David Hewlett) are the only characters to appear in every episode of the series. Sheppard is set to appear in the now in production Atlantis direct-to-DVD movie, set to be released in 2011.

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.

After they discovered that the shield protecting the underwater city of Atlantis was about to collapse, he joined the mission team searching for a new power source on Athos on Elizabeth Weir's orders. He made a better impression on the Athosian leader, Teyla Emmagan. Sheppard then killed the Wraith Keeper, thus awakening all the other hungry Wraith that were sleeping. After retreating with a Puddle Jumper along with other military personnel and rescued Athosians they returned safely to Atlantis.

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