"What are you? Captain Kirk?!"
Dr. Rodney McKay

John Sheppard is an officer in the United States Air Force and, since 2004, a member of the Atlantis Expedition, commanding the expedition's military contingent for much of that time.


Before the Atlantis Expedition

John Sheppard was born to a wealthy family and was the son of Patrick Sheppard, a utilities mogul. By the time he was fourteen years old, his father had already planned his life for him. However, Sheppard had other plans and wanted to join the Air Force, this heavily strained his relationship with his father and never spoke to him since, leaving his brother, Dave Sheppard to take his place. He did mention that he had a university education and admitted to taking a MENSA exam. (SGA: "The Brotherhood", "Spoils of War", "Outcast")

After his education he joined the United States Air Force and participated in several top secret missions, particularly in Afghanistan, but also visited every continent, apart from Antarctica. He trained to become a pilot and could fly several types of Earth-based aircraft, particularly Apache, Black hawk and Cobra helicopters, as well as a V-22 Osprey and an F-16 fighter. He was married to Nancy Sheppard, who worked at Homeland Security in Washington D.C. However, due to spending much of his marriage on secret missions, this led to a strain in their relationship and eventually divorced. (SGA: "Phantoms", "Outcast")

On one of his operations, he initiated a black mark by going on an un-sactioned rescue mission to save one of his friends, Holland from the Taliban in Afganistan. However, he failed to save him and almost got court-martialled because of it. This led people to believe that he wasn't going to advance beyond the rank of Captain, but was eventually promoted to Major. (SGA: "Rising", "The Intruder", "Phantoms")


Sheppard came to the attention of the Atlantis expedition members while serving at McMurdo Air Force Base in Antarctica. While he was flying General Jack O'Neill to the Ancient outpost nearby, he successfully evaded a rogue drone weapon that had accidentally been launched and targeted his helicopter. It was then discovered that Sheppard possessed the ATA gene that gave him an innate ability to control Ancient technology. This led Doctor Elizabeth Weir to insist on his addition to the team. Sheppard was less than enthusiastic about the prospect of traveling through the Stargate to another galaxy, but agreed after O'Neill personally intervened.

Soon after arriving on Atlantis, Sheppard was assigned to a team that came into contact with the Athosians, who were led by Teyla Emmagan. Not long after their arrival, he witnessed the "culling" of the Athosians' village, in which both Teyla and Colonel Marshall Sumner, Sheppard's immediate military superior, were captured.

John Sheppard

Sheppard during his first year with the Atlantis expedition.

Eventually, Sheppard lead a team to rescue Sumner and the captured Athosians. They escaped with nearly everyone, but Sheppard was forced to gun down his own commanding officer in order to keep him from suffering further from the life-sucking power of the Wraith. Sheppard was also able to kill the Wraith Keeper, allowing the Tau'ri and Athosians to escape, but with the unfortunate result of awakening the Wraith from their hibernation cycle fifty years prematurely.(SGA: "Rising")

With the loss of Colonel Sumner, Sheppard was left to command the military contingent of Atlantis. He also took up the command of the expedition's flagship exploratory team, spearheading the expedition's efforts to explore the Pegasus galaxy.

When a Genii strike force under Acastus Kolya tried to take Atlantis, Sheppard waged a one-man war on the invading Genii, systematically sabotaging their efforts and killing fifty-five Genii soldiers by activating the gate shield. The Genii eventually decided to retreat, trying to take Weir and McKay with them. Sheppard was able to save Weir by hitting Kolya in the shoulder, but the incident was the begining of a long animosity between the two soldiers. (SGA: "The Eye", "The Storm")


Months later, he and his team encountered Kolya again on Dagan when they attempted to aquire a Zero Point Module and was captured by Kolya's team. After they found a way out and took out the guards, he let Kolya live, but explained that if they were to cross paths again, he will kill Kolya on sight. (SGA: "The Brotherhood")

Within a year of the Wraith awakening, the Wraith descended on Atlantis, hoping to locate Earth and ending the "uprising" that the Expedition had caused. Shortly before the Wraith attacked the city, Sheppard was relieved by Colonel Dillon Everett, who commanded the defense of the city. The fighting became desperate enough that Sheppard chose to take one of the Puddle Jumpers on a suicide mission to destroy one of the Wraith hive ships in orbit. The mission was successful, and Sheppard was saved by the timely arrival of the Daedalus. With Everett critically wounded by Wraith feeding during the battle, Sheppard worked with Colonel Stephen Caldwell of the Deadalus throughout the remainder of the siege. (SGA: "The Siege")

Not long after the thwarted invasion, Sheppard returned to Earth with several other senior members of the Expedition. At this point, the Pentagon's intention was to replace Sheppard with another, higher-ranking officer with a less spotted record, with General Hank Landry indicating that Colonel Caldwell was the preferred candidate. At the insistence of Doctor Weir, however, Sheppard was instead promoted to Lieutenant Colonel and appointed the expedition's permanent military commander. (SGA: "The Intruder")


Sheppard as a Bug-like creature.

After the event in which he was attacked by Ellia, who was injected with the Iratus bug retrovirus, but made her more into a bug rather than human, she transfered some of the retrovirus into him before getting killed. He started to notice that his wound was healed much faster than usual. He later noticed that his former wound is slowly transforming him into a bug-like creature. Beckett attempted to slow it down by an inhibitor, but was eventually transformed. They also tried to grab some of the eggs of the Iratus bug to reverse the transformation, but couldn't get close. The team was about to say goodbye to him, until Beckett realised that John has the pheromone to stop the bugs attacking. He was able to get the eggs and transformed back to Human again. (SGA: "Instinct", "Conversion")


Sheppard had his conscioussness taken over by Thalen, who wanted to kill Phoebus, who was Thalen's enemy and took control of Weir. They attempted to kill each other, risking the Expedition in the process. Thalen's conscioussness expired first, and Sheppard was able to stun Phoebus, before she would kill him. (SGA: "The Long Goodbye")

During the fake alliance the Wraith proposed, Sheppard attempted to fight off two Hive ships, but was taken into hyperspace, heading for Earth. The Daedalus' crew thought that he had disappeared, but actually attached his F-302 on one hive and helped stop the hive ships from taking off again in the Battle of the Void. (SGA: "Allies", "No Man's Land")

After a year and a half from last seeing him, he was once again captured by Kolya, who wanted to exchange him for Ladon Radim, since it was Kolya who actually planned a coup against Cowen. Kolya also captured a Wraith, later to be known as "Todd" to fed a little off his life. He must have aged a further 30 to 40 years. However, an aged Sheppard convinced the Wraith to join forces and escaped from the compound. Todd was able to return all the years he took from him. Sheppard decided to drop him off on another planet and spared his life, but he let Kolya get away again. However, a few more months later, Sheppard kept his word and killed Kolya in a duel. (SGA: "Common Ground", "Irresponsible")


After Atlantis tried to escape Lantea from the Asuran Stargate satellite weapon, the beam grazed the tower and incapacitated Weir. When Atlantis was stranded in deep space with 24 hours of power left, he was appointed the commander in charge, and went with McKay, Ronon, Teyla and Weir to Asuras to steal a ZPM and upload a programme that would make the replicators attack the Wraith, but lost Weir in the process. His command was replaced by Colonel Samantha Carter. He was actually on the short list, but the command was given to Carter in the end. Sheppard didn't mind, as he said he never wanted the job. (SGA: "First Strike", "Adrift", "Lifeline", "Reunion")

Whilst he was on a routine resupply mission to an offworld base, his Jumper was disabled and was kidnapped by a race of people he would know as Travellers. They needed him to power a stranded Aurora class warship to help the race's population troubles. He sent the ship into hyperspace, but was later attcked by the Wraith. He worked with Larrin to deter the Wraith from the ship and was released when he proposed an alliance. (SGA: "Travellers")

He encountered "Todd" again, who proposed an alliance when the Asurans were wiping out Human worlds to stop the Wraith. They worked in trying to shutdown the nanite base code. After McKay and his sister was kidnapped, he helped in breaking them out. However, nanites would kill Jeannie, and "Todd" almost finished on a away to shut down the nanites, until he collapsed and needed a Human to feed on. Sheppard turned to Henry Wallace, the kidnapper, who lost his daughter due to the nanites. He convinced Wallace to sacrifice his own life in order to shut down the Asurans. (SGA: "The Seer", "Miller's Crossing")


Sheppard heard that his father died of a heart attack, and came to attend his wake. It was there that he learnt that his father regretted the argument they once had that drove them apart. He also coerced his ex-wife, Nancy into helping find information on Project Archetype to track down a replicator loose on Earth. (SGA: "Outcast")

After Teyla was catpured by Michael Kenmore, he vowed to bring her back. In one instance, he travelled back to Atlantis 48,000 years in the future. However, a hologram of McKay managed to have brought him back in the present, with a gate adress to M2S-445, a planet Michael was planning to kill Teyla. However, he arrived too early, and the building collapsed on him and his team. He was seriously injured, but was still adamant to rescue Teyla. He managed to do so. After the successful mission, he was taken into surgery. He was highly honoured that Teyla was to name her baby Torren John, partly named after him. (SGA: "The Kindred", "The Last Man", "Search and Rescue")

Alternate realities

  • In an alternate reality John Sheppard traveled to Atlantis, while the power began to fail and the city began to be flooded by the ocean. Upon finding the bay of Puddle jumpers, he suggested they be used a escape vessels. Sheppard, Elizabeth Weir, and Radek Zelenka boarded a jumper different from the others: it was carrying a time machine in it. Sheppard activated the time machine, sending them back to the time of the Ancient-Wraith war, when the city was under seige. They came under attack by a pair of Wraith Darts. Though Sheppard managed to take out one of the darts, the other shot them down. Sheppard and Zelenka were killed in the crash, but Weir survived. (SGA: "Before I Sleep")
  • In an alternate reality John Sheppard is active with the Mensa club on Atlantis. He keeps reminding Rod McKay of his intelligence, making the Rodney McKay of our reality modest by comparison. (SGA: "McKay and Mrs. Miller")
  • In an alternate reality, Sheppard's team went onboard the alternate Daedalus and starved to death onboard the runaway ship. (SGA: "The Daedalus Variations")
  • In an alternate reality, Sheppard led a squadron of F-302s to defend the alternate Daedalus from alien fighters. (SGA: "The Daedalus Variations")


  • John Sheppard has the ability to instantly calculate certain difficult equations. For instance in the season 1 episode Home he instantly knew it would take a Puddle Jumper 840 years to get to M5S-224 if Mckay broke the DHD. However, it is possible that he looked this up beforehand.
  • John Sheppard is played by Joe Flanigan and has appeared in every episode of Stargate Atlantis to date.
  • Ben Browder was originally planned to play the part of Sheppard. However, Flanigan took his place, after Browder was busy with Farscape: The Peacekeeper Wars, and would later play the part of SG-1 regular, Cameron Mitchell.

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