Lieutenant Colonel is an
Air Force officer played by
Joe Flanigan in the television series ''
Stargate Atlantis ''.
Sheppard is an experienced pilot and second-generation military man, though his reputation was somewhat tarnished when he disobeyed a direct order in Afghanistan in an attempt to save the lives of several servicemen. He requested a remote post at
McMurdo Station . When called upon to transport General
Jack O'Neill to the research base that had been established at the nearby
Ancient defence 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 the gene. After some doubts, he finally joined the expedition to
Atlantis , although Col.
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
Dr. Weir 's orders. He made a better impression on
Teyla than Sumner; she showed him a cave with old carvings that explained the
Wraith attack many generations ago. When the Wraith attacked, Teyla saved him, but was scooped herself by a
Wraith Dart . He evacuated the Athosian refugees to Atlantis while Atlantis was rising to the surface. After a discussion with Dr. Weir, he and several others led a rescue mission to save the captured Earth personnel and the Athosians. After infiltrating the Wraith hive ship, he found Colonel Sumner near death at the hands of the Wraith Keeper, and killed his superior officer to spare him from more suffering. He was then captured by the Wraith, but Ford arrived in time to save him from the same fate. Sheppard then killed the Wraith Keeper, thus awakening all the other ravenously hungry Wraith that were sleeping and earning the enmity of the entire Pegasus Galaxy. After some fancy flying with the
Puddle Jumper , he, his team and the rescued Athosians returned to Atlantis, when he found himself the highest-ranking military officer present ("
Rising ").
Aside from being the ranking military officer, Sheppard leads an exploration team that consists of Dr.
Rodney McKay , Lt.
Aiden Ford and
Teyla Emmagan .
After McKay acquired the ATA gene, Sheppard helped him test an invulnerability shield device, by shooting Rodney in the leg and throwing him off a balcony. Afterwards, when
Jinto unknowingly let loose an energy creature, he tried to capture it, but the creature didn't fall into the trap (
Hide And Seek ).
On a later mission, Sheppard was bitten by an
Iratus Bug (a Wraith-related parasitic insect) that was slowly draining him. His puddle jumper got stuck in the Stargate when the pods failed to retract correctly, and the only way to get the bug off of him was to stop his heart with a
Defibrillator . It worked, but they could not get his heart started again. Teyla took him to the event horizon of the Stargate, which effectively "froze" him in time until the jumper was able to get through it. Once in the other side, Dr.
Beckett and his team managed to restart his heart (
Thirty-eight Minutes ).
He fought the invading Genii single-handledly to save McKay, Weir and the city of Atlantis. He took out several of them before Ford, Beckett and Teyla arrived to help. When the Genii dialed to get more people in Atlantis, he raised the Stargate's
Iris , killing more than fifty Genii soldiers at once. When
Kolya took Weir as a hostage as he fled the city, Sheppard shot him in the shoulder; Kolya let go of Weir and fell through the event horizon. They later learned he survived. (
The Storm/The Eye )
In the episode (
The Brotherhood ), he revealed that he passed the
Mensa exam (through the way of figuring out the puzzle of the Brotherhood of Fifteen), but decided not to join.
During the Wraith attack on Atlantis, Sheppard lost command of the military after the arrival of Colonel
Dillion Everett from Earth. Everett was a good friend of Colonel
Marshall Sumner and was hostile to Sheppard because of Sumner's death. During the first wave of the attack, Sheppard sat on the control chair and used the remaining
Drones to help fight the darts off. After the drones ran out, McKay and
Zelenka tried to link the chair to the puddle jumpers, so the chair could be used to pilot them remotely to deliver
Genii -made
Nuclear Bomb s inside the Wraith hive ships. As the time ran out, the chair failed to work and Sheppard decided to pilot the jumper himself on a suicide mission. ("
The Siege, Part 2 ")
Major Sheppard was saved by the timely arrival of the
''Daedalus'' , which transported him out of the puddle jumper seconds before it exploded. After the Daedalus destroyed the remaining hive ship, Sheppard returned to Atlantis, where a Wraith-aged Col. Everett told him that now he understood what happened with Col. Sumner and that he wished Sheppard would have been there for him.
When Dr. McKay and Dr. Zelenka discovered 12 more hive ships were traveling through hyperspace to Atlantis, he proposed to use the Daedalus to attack them before they arrived, and Weir agreed. They took two hive ships out, but they were forced to retreat. Once the new hive ships arrived at Atlantis, Sheppard had the idea (thanks to a comment from Dr. Zelenka) to make the city disappear so the Wraith would leave thinking it had been destroyed. McKay and Zelenka were able to implement the plan, and this time it worked. After Ford escaped from the infirmary, Sheppard tracked him down with a Wraith stunner but was unable to stop him, and Ford fled through the Stargate ("
The Siege, Part 3 ").
After securing Atlantis, the Daedalus took Sheppard, Weir, McKay and Beckett back to Earth to report. General
Hank Landry implied to Weir that the Pentagon wanted to make Col.
Steven Caldwell military commander, but Weir informed them that Atlantis already had a military commander, John Sheppard. When they stated that Sheppard was just a Major with a questionable record, she told them they could solve that problem -- with the
President and the International Committee on her side, Sheppard was promoted to the rank of Lieutenant Colonel, and remained military commander of Atlantis. This annoyed Col. Caldwell, who had sought the leadership position.
On the voyage back to Atlantis, the Daedalus was infected by a Wraith computer virus, which made the ship send a distress signal they couldn't stop. Sheppard used a
F-302 fighter to destroy the transmitter array, but the virus had control of the plane and he could not return to the Daedalus until they transported him out. Later, when McKay figured out that the virus was using the computers of the F-302 fighters to store itself to prevent removal from the system, Sheppard and McKay had to physically remove all memory units from the fighters. The virus tried to decompress the fighter bay to kill them, but they boarded one F-302 to survive. When, after clearing all of the fighters' systems, another system reset still failed to clear the virus, Sheppard deduced that the virus was using the F-302 he was beamed out of earlier, which has been tailing them, to re-upload itself to the Daedalus. He took a stripped F-302 out, with McKay in the back seat, and managed to destroy the infected fighter after some fancy flying. ("
The Intruder ")
Soon thereafter, while exploring a planet, a team discovered Lt. Ford's whereabouts. Before leaving for the planet, Caldwell reminded Sheppard that Ford was a significant threat to the security of the base and, if he could not capture him, he was duty-bound to eliminate him. On the planet, Sheppard and Teyla were taken by a mysterious man called
Ronon Dex , a
Runner , who had an implant which allowed the Wraith to stalk him. After they offered to have Dr. Beckett remove the tracking device, Dex agreed to assist them in finding Ford in return. Later, Ronon returned to Atlantis with them. ("
Runner ") Once there, after seeing Ronon sweep the floor with the Marines and pass the shooting range without even blinking, Sheppard offered him a place on his team. ("
Duet ")
After their first try at reactivating
Project Arcturus went wrong, Sheppard backed McKay to return to the project, after McKay asked Sheppard to trust him. McKay failed spectacularly, and 5/6ths of a solar system was destroyed as a result. McKay later told Sheppard he hoped he could earn his trust back and Sheppard answered that it might take a while, but that he was sure Rodney could do it if he really wanted to. ("
Trinity ")
Sheppard and his team travelled through an orbiting Stargate to a planet unused to visitors, where they found a young female Wraith who, it seemed, didn't feed on humans, as she had been raised as a daughter by a human scientist. Wanting acceptance among the humans, she stole Dr. Beckett's not-yet ready retrovirus which, instead of turning her into a human, stripped all humanity from her. Sheppard fought and killed her, but not before she infected him with the retrovirus. ("
Instinct ") Upon his return to Atlantis, they discoverd that the retrovirus had begun to change Sheppard into a humanoid
Iratus Bug . As the mutation progressed, his strength and stamina increased, his skin started to change, his eyes became yellow with slitted pupils, and he gained the ability to crawl up walls.
Dr. Weir forbade him to accompany the team on the mission to retrieve Iratus eggs to research a cure. When she later visited him in his room to tell him the mission had failed and that she was not going to send another team since they had lost two Marines, the heavily-mutated Sheppard attacked her and escaped. After a chase, Ronon finally stopped him; Sheppard was then returned to the infirmary, restrained, and drugged into a coma while the team continued to research a cure. Dr. Beckett deduced that the eggs were the only hope, and moreover, due to physiological makeup, Sheppard was the only one who could retrieve them, he was awakened to go with the team and Beckett to the planet. He managed to retrieve the eggs before the retroviral inhibitor Beckett gave him lost effect. The treatment worked, and he returned to normal in two weeks. ("
Conversion ")
The Atlantis team found an Ancient ship, the Aurora, with all the crew in suspended animation. They were too old to survive outside of the stasis pods, but Dr. McKay discovered that they were living in a kind of virtual reality. Sheppard entered a stasis pod and accessed the virtual reality in order to try to discover the information about a Wraith Achilles' heel the ship had been carrying back to Atlantis. However, the crew was unaware that they were in a virtual reality, and didn't believe him. While Sheppard was in the simulation, Teyla discovered that a Wraith had infiltrated the VR system. Finally, Sheppard convinced the captain of the Aurora of the truth of their situation, but the captain was unable to turn over the intelligence data since the Wraith infiltrator had succeeded in destroying it. He then gave Sheppard the ship's auto-destruct code, since two Wraith cruisers were on their way to intercept. The Daedalus transported the Atlantis team onboard after they executed the auto-destruct sequence, and the Aurora exploded, destroying the Wraith cruisers. ("
Aurora ")
Soon afterwards, Sheppard and his team were captured during a mission by Lt. Ford and a band of fellow Wraith enzyme addicts he had gathered. Ford wanted them to recognize the Wraith enzyme as an asset, and proceeded to dose Teyla, McKay and Ronon with it, leaving Sheppard clean as a control. Ford planned to use a captured Wraith dart to infiltrate a hive ship and destroy it, as proof of the enzyme's benefits, and he needed McKay to fix the dart and Sheppard to fly it. Sheppard convinced McKay to go along with the plan, telling him that, once they were aboard the dart, they would escape to Atlantis. But Ford foiled his plan by breaking his promise and leaving McKay behind on the planet. Sheppard was forced to fly the dart, with Teyla, Ronon, Ford and some of Ford's men dematerialized inside. Once the dart arrived near the hive ship, however, an automatic pilot took control to get them inside and rematerialized the people. Two of Ford's men fell into the void because the platform was too narrow, and Ford didn't believe that Sheppard hadn't done it on purpose.
The mission quickly went wrong and they were all captured. Sheppard was brought in front of the Wraith Queen, who was unable to get any information out of him. They managed to escape the cell, freeing a captured woman, Neera, of a cocoon on the way, but they were then recaptured. Sheppard and Neera were placed together in a cell, and Sheppard became suspicious of her after she began questioning him. His suspicions were proven correct after he was, again, brought in front of the Wraith Queen, who revealed to him that Neera and her people were Wraith worshippers, whose lives where spared in exchange for service. Ford rescued him, but remained behind to cover his escape. After sweeping Teyla and Ronon up with the dart again, he fled the hive ship. Outside, he attacked the other hive ship, making the two ships believe that the other was firing on them and causing them to destroy themselves. The team returned to Atlantis, and despite the destruction, Sheppard was sure they would see Ford again. ("
The Lost Boys " and "
The Hive ").
Soon after, while looking for an energy spike Dr. McKay had detected, they found a cave whose entrance was protected by a kind of force field. Col. Sheppard moved towards the field, that pulled him in and into the cave. Strangely, nobody followed him but some time later he received a bag with provisions. They didn't last long and some days later, angry with his friends, he decided to move away from the cave. He saves a man, Avrid, from a strange energy Beast but it's hurt in the process. He wakes up in Avrid's home being cared for by his sisters, and he learns all the people in the village are working for Ascension and that there's no way out the Sanctuary. John eventually settled into the life of the Cloister, becoming very close to Avrid's sister Teer, but he kept looking for a way out. When the rest of his team, plus Dr. Beckett and Dr. Weir, finally arrived, six months has passed for him but only a couple of hours for them, since the Sanctuary turned out to be a time dilation field constructed by the Ancients to help people looking for Ascension. Sheppard's example finally prompts the Cloister's people to confront the Beast themselves. The Beast was a manifestation of their own fears and, once vanquished, they were able to finally Ascend. Teer offers him to accompany them, but he refuses. She told him, however, that they will keep the time dilation field open until they leave ("
Sanctuary ").
