Lieutenant Colonel in the United States military and a highly skilled pilot with a checkered past, John Sheppard commands the flagship reconnaissance team from Earth's Atlantis base. He traveled to the Pegasus Galaxy with the Atlantis expedition under the command of Dr. Elizabeth Weir, and became the base's ranking military officer following the death of Colonel Marshall Sumner at the hands of the Wraith. He leads the base's flagship reconnaissance team in exploring other worlds through the Stargate.
Sheppard was based at McMurdo Air Force Base -- possibly due to the black mark on his record -- and preferred the quiet of the Antarctic. He was assigned to fly General Jack O'Neill to the remains of the Ancient outpost to oversee the research team's latest developments. There he discovered that he possesses the rare gene that allows him to use Ancient technology -- and unlike most others who possess the gene, he is a natural at it. Weir implored O'Neill to allow Sheppard to be a part of her team despite his record, tarnished for disobeying orders to save two teammates in Afghanistan.
Once in the Pegasus Galaxy Sheppard was sent on a mission to planet Athos in the hopes of recovering additional Z.P.M.s to power the sunken city of Atlantis. He met the Athosian leader Teyla Emmagan and her people, and the two immediately hit it off. He learned of the threat of the Wraith, who had once defeated the Ancients, and witnessed a culling of the Athosians -- including Teyla -- and Sumner, his commanding officer. Sheppard returned to Atlantis with the surviving Athosians, and embarked on a daring rescue mission to recover them. He was successful -- but in the process, Sheppard was responsible for reawakening the entire Wraith civilization when he killed the Wraith Keeper.
As the most senior surviving member of the Atlantis expedition's military contingent, John served as the head of the officers stationed there -- making him second in command of the base, to the civilian Weir. One year later he was promoted to Lt. Colonel, when his role on Atlantis was formalized. He was on the short list to assume command when Weir was lost to the Replicators, but seemed happy to have Colonel Samantha Carter take the job instead.
Sheppard enjoys ferris wheels, college football, and "anything that goes faster than 200 miles per hour." He loves Johnny Cash and is kind and generous, and not afraid to voice his opinions, particularly when the end result is in the best interests of a needy teammate. Little is known about his past or family life, though he was once married.
Rising, Part 1 - A simple, past-stricken helicopter pilot is caught up in an adventure of galactic proportions when he travels to the Pegasus Galaxy and encounters a kind people, as well as a vampirous new enemy.
Rising, Part 2 - Sheppard leads a rescue mission to save his people and Athosian captives from the Wraith, but must kill his commanding officer to spare Sumner from the Wraith's life-sucking torture.
Thirty Eight Minutes - Major Sheppard's life is threatened when a Wraith-like insect attaches itself to his neck.
Underground - Sheppard tries to forge and alliance with the Genii, but makes an enemy out of them instead.
Home - John becomes suspicious when everything is even better than it should be on a return trip to Earth.
The Storm - When Atlantis is occupied by a Genii strike force, Sheppard plays a deadly game of cat-and-mouse with Commander Kolya and his people.
The Eye - Sheppard helps to drive the Genii out of Atlantis, but makes a personal enemy of Acastus Kolya.
Sanctuary - John falls for a beautiful alien woman, only to discover that she is an ascended being.
The Intruder - John Sheppard is promoted to Lieutenant Colonel.
Conversion - Colonel Sheppard undergoes a disturbing physical transformation after being exposed to Beckett's anti-Wraith drug.
Epiphany - John is stranded on a planet where time passes more rapidly, with no way to contact his friends -- and where the locals are threatened by an invisible monster.
The Long Goodbye - Sheppard is possessed by an alien entity, who is at war with an entity who has possessed Dr. Weir.
The Real World - John risks exposure to deadly Replicator nanites in order to help Elizabeth escape their hold.
Common Ground - Sheppard is captured by Commander Kolya, who uses a Wraith to slowly drain the life out of him. But the two prisoners form an alliance and escape.
Phantoms - A mind-altering device causes Sheppard to relive a mission from his past.
Irresponsible - Sheppard goes toe-to-toe with Kolya one last time, shooting him dead in a duel.
Adrift - Sheppard is forced to assume command of Atlantis after Weir is incapacitated by her injuries.
Doppelganger - An alien entity takes on Sheppard's image when it appears in his friends' nightmares, forcing John to fight himself.
Travelers - John is captured by a group of technologically advanced humans, led by the beautiful Larrin, who demands that he help them activate a derelict Ancient warship.
Quarantine - When a computer malfunction causes a city-wide lockdown Sheppard has to climb up the outside of Atlantis to get to the control room.
Outcast - Sheppard returns to Earth to attend his father's funeral, and meets a scientist with a major problem, a rogue human-form Replicator.
The Last Man - An accidental interaction between a wormhole and a solar flare sends Sheppard forty-eight thousand years into the future.
The Shrine - Sheppard assists Doctor Keller in an operation to remove an organism from McKay's brain.
Remnants - During an expedition to the mainland Sheppard is captured and tortured by a man he thought he had killed, Acastus Kolya.
Vegas - On an alternate reality Earth, police detective John Sheppard must solve the case of a long string of unusual murders.
Enemy at the Gate - With a Wraith super-hive ship fast approaching, Sheppard is sent to Earth to man the control chair, which is now housed in Area 51.