John Sheppard

"What are you? Captain Kirk?!"

- Dr. Rodney McKay

John Sheppard, also known as "Guide" among the Wraith society, 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.

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 for a large variety of aircraft. such as the Apache, Black hawk and Cobra helicopters, as well as a V-22 Osprey and an F-16 fighter, indicating that he graduated from Test Pilot School. 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.

On one of his operations, he initiated a black mark by going on an unsactioned rescue mission to save the lives of three servicemen. Another unsanctioned Op was to save the life of his friend, Captain Holland, whose Apache had crashed in Afghanistan. The mission, however, was unsuccessful. He was later forced to relive this memory when his team went to find out what happened to Major Leonard's team in "Phantoms."

2004
"You do realize I could get us into all sorts of... trouble, right?"

- Sheppard about himself after Elizabeth Weir reminded of him of his status as Atlantis' military leader

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.

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.

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 when they attempted to send reinforcements through the Stargate. 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.

2005
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.

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 Steven Caldwell of the Daedalus throughout the remainder of 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.

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.

2006
Sheppard had his conscioussness taken over by Thalan, who wanted to kill Phoebus, who was Thalen's enemy and had taken 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.

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.

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.

2007
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 and Weir to Asuras to steal a ZPM and upload a program 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.

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 battleship to help the race's population troubles. He sent the ship into hyperspace, but was later attacked by the Wraith. He worked with Larrin to deter the Wraith from the ship and was released when he proposed an alliance.

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 were kidnapped, he helped in breaking them out. However, nanites would attempt shut down Jeannie to heal her of her epilepsy. "Todd" was 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 had lost his daughter due to the nanites. He convinced Wallace to sacrifice his own life in order to shut down the nanites.

2008
Sheppard heard that his father died of a heart attack, and came to attend his wake. It was there that he learned 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.

After Teyla was captured 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 on. 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.

2009
Colonel John Sheppard came to Earth to operate the Ancient Control chair in an effort to defend Earth against Kenny's ZPM powered hive ship at the Battle of the ZPM powered Hive Ship. When the chair was destroyed by a kamikaze attack by the Wraith, he flew an F-302 armed with a nuclear warhead to the "Super hive" in an attempt to destroy the ship in a suicide attack. Before he could act, he learned that a team had arrived from Atlantis in an effort to sabotage the ship. With them, he activated the nuclear warhead remotely and escaped via the on-board Pegasus Stargate.

Talents and abilities
John was one of the most skilled fighters in Atlantis. He was able to use a wide a variety of Tau'ri and Wraith weapons. He was taught many Pegasus fighting styles by both Teyla and Ronon, although he regulary loses to the more experienced fighters. When the Genii temporarily seized control of the city he was able to drive them out almost single-handedly.

He is an exceptionally skilled pilot, being able to fly a wide variety of ships, ranging from Wraith darts to Ancient City-ships. In fact, he has either piloted or assisted in piloting almost every known ship in the Pegasus Galaxy. He ranked first on the Chair Interface Aptitude list in Atlantis, which gave him a natural ability to pilot Ancient ships. He is a skilled fighter pilot, often flying an F-302 in space combat. His skill with Wraith darts is less than with other vehicles, due to the unusual nature of Wraith technology and his lack of of experience. Before flying Atlantis the largest thing he had ever flown was a V-22 Osprey. Despite having no psychic abilites beyond his ATA gene, John has one of the most powerful mental defenses known. He is able to resist Hive Queens and Asuran mind-probes, albeit with difficulty. When AR-1 was temporarily placed in a mental illusions by the inhabitants of M5S-224 John displayed the ability to manipulate his own illusion, and was aware that something was wrong almost immediately. By 2008 he was able to completly resist a Queen, although it cost him a visible effort to do so. The Queen claimed he had the strongest resistance she had ever encountered from a human.

John is also a keen and talented golfer, although he is disappointed that no-one else on his team shares his enthusiasm.

Relationships
Prior to coming to Atlantis, John's ability to form meaningful relationships with others was poor; he and his father hadn't spoken with each other for several years, and his marriage had fallen apart due to his inability to be there for her. However, since arriving in Atlantis, he has formed close bonds with several people, ranging from the senior staff to offworld allies.

Larrin
Shepard first met her when she used a Traveler's ship to disable Shepard's jumper and later captured him to use him to activate a Aurora-class Atlantean battleship. At first they hated and distrusted each other. But after working together to rid the ship of Wraith and Shepard saved Larrin's life from a Wraith that fed on her. She then thanked him and kissed him. Larrin later fought in the battle against the replicators. When it was over Shepard asked for a means of contacting her for "professional" reasons. He later ran into some Travelers and asked the captain if Larrin ever mentioned him. She later mentioned she did. It is implied that should they meet again that their relationship might develop into something more.

Elizabeth Weir
Although she initially only recruited Sheppard for his powerful ATA gene, Elizabeth Weir came to greately respect John's abilities as a soldier, particularly after he single-handedly saved Atlantis from a Genii invasion. When Colonel Dillon Everett arrived to take command of Atlantis following Earth's discovery of a new Zero Point Module and the news of the approaching Wraith Hive-ships, it was John who convinced Everett to keep Elizabeth in the loop if he wanted to maintain the support of the rest of the city. Elizabeth reciprocated this respect by insisting that John be promoted to Lieutenant Colonel rather than allow someone else to take command of Atlantis after the expedition regained contact with Earth. Elizabeth continued to visit John even after he began to mutate into a Wraith-like creature following his confrontation with Ellia and the mutated Iratus bug retrovirus, John reciprocating this compassion by risking his life to try and urge her to keep fighting after she was infected by Asuran nanites during her enounter with Niam. John was clearly deeply affected by Elizabeth's loss when he was forced to leave her behind on the Asuran homeworld, and his grief when he learned that she was dead--having first heard a second-hand account from the Organic Asuran duplicates of his team and subsequently witnessing her return and sacrifice to defeat the remaining Asurans--was particularly pronounced, hinting at the strong bond between them that was never given the chance to develop into something more.

Atlantis Team
Easily the closest bonds John has formed since coming to Pegasus are the bonds he shares with his teammates on AR-1, although he and Doctor McKay are prone to the occasional argument, with McKay sometimes growing frustrated with John's apparent assumption that he can automatically save the day when scientific problems arise. The two have shown on many occasions that they have both a great esteem for the other's abilities and share a surprisingly close bond, with McKay commonly attempting to help John when he suffers from personal problems despite his own poor abilities with relationships, such as when he attempted to express his sympathies following the death of John's father. The two have also been shown to spend a surprising amount of their leisure time together, both of them playing what they initially believed to be a Civ-like game before learning that it was an Ancient experiment with real people, and racing RC cars in the lower halls of Atlantis.

The most obvious bond he has formed on his team is his friendship with Ronon, which has been compared by many to the bond between Jack O'Neill and Teal'c. Both featuring human military leaders forming close bonds of respect and loyalty with alien soldiers who obey the other out of respect rather than adherence to the chain of command. The two men have been seen as having an almost brotherly relationship, Ronon leading the search for John when he was captured by Commander Kolya and later accompanying Sheppard back to Earth for his father's funeral. His friendship with Teyla Emmagan is another example of his ability to bond with others despite different backgrounds, believing in Teyla even when evidence suggested that she was feeding information to the Wraith--both deliberately and unintentionally--and showing great concern for her during her pregnancy. Teyla even named her son after him.

Although his bond with Lieutenant Aiden Ford never developed beyond simple friendship. John nevertheless clearly thought a great deal of the younger man, refusing to kill him even after he was driven half-insane by his use of the Wraith enzyme, and taking three years following their last encounter before he 'admitted' that Ford was almost certainly deceased.

At one point he admitted that he didn't really have a family and his team and Weir were the closest thing he had to one.

Family
Sheppard is mostly estranged from his family. He had a wife, but they divorced after she couldn't take all of the secrets, although she did later come to understand how hard it must have been for him. His father and brother are successful businessmen and his father wanted him to be one too and they had a falling out when he wanted to join the Air Force. Sheppard felt he wasn't welcome by them afterwards and seemed to think he had no family as a result. He did return for his father's funeral and his brother thought he only wanted money from their father's will after being gone so long. His brother, Dave, revealed to him that his father always regretted their fight and wanted to make up but never got the chance, which seemed to stun John. After stopping a Replicator threat, John returned home to make up with his brother who seemed to accept him back into his life.

Alternate realities

 * In an alternate timeline, when the Expedition traveled to Atlantis, the power began to fail and the ocean began flooding into the city. Upon finding the bay of Puddle Jumpers, Sheppard suggested they be used as escape vessels. He, along with Elizabeth Weir and Radek Zelenka, boarded a jumper different from the others: it was carrying a time machine. Sheppard activated the time machine, sending them back to the time of the Ancient-Wraith war, when the city was under siege. They came under attack by a pair of Wraith Darts. Though Sheppard managed to destroy one of the darts, the other shot them down. Sheppard and Zelenka were killed in the crash, but Weir survived.
 * In an alternate reality, John Sheppard is active with the Mensa club on Atlantis. He constantly reminds Rod McKay of his intelligence, making the Rodney McKay of our reality modest by comparison.
 * In an alternate reality, Sheppard's team boarded an alternate Daedalus and starved to death onboard the runaway ship.
 * In an alternate reality, Sheppard led a squadron of F-302's to defend the alternate Daedalus from alien fighters.
 * In an alternate reality, John was dishonorably discharged after attempting to rescue an unnamed medic, who he was romantically involved with, in Afganistan (this differs from our reality where he tried to save Lyle Holland). His helicopter was shot down and the crash killed four American soldiers and eight civilians. After narrowly escaping jail time for political reasons, he moved to Las Vegas where he joined the LVPD. He was $13,000 in debt due to a gambling problem and only had about $2300 in his bank account. After four years of trying, he was finally promoted to Detective. Though this alternate version of John Sheppard was never married, he is still a fan of Johnny Cash, taking only a poster (the same one seen in his quarters on Atlantis) with him after resigning his position. While leaving town, he figured out where to find the Wraith that had been building a transmitter and tracked it down. He called an alternate version of Rodney McKay who sent two fighter jets to destroy the Wraith's transmitter, but not before John was shot in the chest. He is presumed dead because while trying to crawl away from the wreckage of the destroyed transmitter. He fell to the ground in the middle of the desert and was unable to move any farther. His fate was not revealed, though he appeared to be suffering severe blood loss. It is entirely possible that he perished shortly afterward 

Behind the Scenes

 * John Sheppard and Rodney McKay are the only two characters to appear in every episode of Stargate Atlantis.
 * 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. Browder would later play the part of SG-1 regular, Cameron Mitchell.