Post by Izabella Riddle on Oct 27, 2006 2:31:23 GMT -5
Season 1
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, just seconds before that Atlantis rose to the surface. After a discussion with Dr. Weir, he 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. 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.
Aside from being the ranking military officer, Sheppard lead an exploration team that consisted of Dr. Rodney McKay, Lt. Aiden Ford and Teyla Emmagan. Sheppard's relaxed commanding style often put him at odds with his more by the book chief of security, Sgt. Bates, until a beating by a Wraith forced Bates to return to Earth.
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 did not fall into the trap.
Major SheppardOn a later mission, Sheppard was bitten by an Iratus bug 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 turned out to be 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.
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 shield, 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 Kolya survived, when he captured them while they were trying to find the location of a ZPM. While trying to solve a puzzle, Sheppard revealed that he took the Mensa exam and, though it is implied that he passed (he solved a complex puzzle by recognizing it from the Mensa test), his results have never been revealed.
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 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 bombs 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.
Season 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 and shot him with a Wraith stunner but was unable to stop him, and Ford fled through the Stargate.
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 Oversight 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.
Season Two
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 they had to transport 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 another system reset still failed to clear the virus, Sheppard deduced that the virus was using the hard drive of the F-302 he was beamed out of earlier, which has been tailing them. He took the stripped F-302 out, with McKay in the back seat, and managed to destroy the infected fighter after some fancy flying.
Soon thereafter, Major Lorne's team discovered Lt. Ford's whereabouts. When they arrived 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. Ronon returned to Atlantis with them and, after seeing him sweep the floor with the Marines and pass the shooting range without even blinking, Sheppard offered him a place on his team.
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.
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, did not feed on humans, as she had been raised by a human herbologist as his own daughter. 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. 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.
Sheppard was confined to his rooms but, when Dr. Weir visited him, the heavily-mutated Sheppard attacked her and escaped. After a chase, Ronon finally stopped him; Sheppard was then returned to the infirmary, restrained, and sedated while the team continued to research a cure. Dr. Beckett deduced that Iratus 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 a team 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.
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 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 did not believe him. Meanwhile, Teyla discovered that a Wraith had infiltrated the VR system. Sheppard was finally able to convince the captain of the Aurora of the truth of their situation, but the Wraith infiltrator had succeeded in destroying the intelligence data. As two Wraith cruisers were on their way to intercept the ship, the captain gave Sheppard the ship's auto-destruct code. Once safely onboard the Daedaulus, the Aurora exploded, destroying the Wraith cruisers.
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, 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 did not 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, but the interrogation was interrupted by the emergence of a second hive ship from hyperspace before she could get any information out of him. Sheppard and his teammates managed to escape their cell, freeing a captured woman, Neera, from a cocoon on the way, but they were then recaptured. Sheppard and Neera were placed in a cell together, 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.
Soon after, while looking for the source of an energy spike, they found a cave whose entrance was protected by a kind of force field. 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 did not last long and some days later, angry and hungry, he decided to move away from the cave. He got hurt while saving a man, Avrid, from a strange energy Beast. He woke up in Avrid's home being cared for by his sisters, Teer and Hedda, and he learned all the people in the Sanctuary were working for Ascension and that there was no way out. Six months passed for him before the rest of his team, plus Beckett and Weir, arrived, but it only have been a couple of hours for them, since Sanctuary was really a time dilation field constructed by the Ancients to help people looking for Ascension. The Beast was a manifestation of the Cloister's people fears and Sheppard's example finally prompted them to confront it. Once vanquished, they were able to finally Ascend. Teer offered John to accompany them, but he refused. She told him, however, that they will keep the time dilation field open until they left.
When an accident trapped Dr. McKay underwater in a broken Puddlejumper, Col. Sheppard and Dr. Zelenka took another Puddle Jumper down to help him. Sheppard convinced Zelenka to change the Jumper's cloak into a shield that would allow them to stand the high underwater pressions. The mission was a success and they rescued McKay safely.
When Michael, the Wraith turned human turned Wraith again, approached Atlantis with an offer of information in exchange of Dr. Beckett's retrovirus, Atlantis reluctantly agreed. It turned out to be a trap, and Sheppard was forced again to pilot a F-302 against a hive ship. When the two hive ships went into hyperspace, John disappeared with them.
Season 3
John managed to use the 302 docking clamps to attach himself to a Hive ship. With Michael's help, he damaged the hive ship's hyperspace engines and boarded it to rescue McKay and Ronon. They boarded a Wraith transport and communicated with the Daedalus, which beamed them onboard. The Daedalus was severely damaged, however, and they were forced to use Dr. Beckett's retrovirus to turn the Wraith into humans and take over their hive ship.
They used the hive ship to get back to Atlantis and decided to settle the amnesiac former Wraith into an uninhabited planet. When they returned to the planet, they discovered that some of the humans were turning back into Wraith and he ordered McKay to fire on the planet, using the Hive ship's energy weapons to destroy them. They were forced into battle by another hive ship, and theirs was destroyed (it is not clear what happened to the other ship), but they managed to save themselves using a Puddle jumper, and they were rescued by the Daedalus.
When Sheppard met Cameron Mitchell of SG-1, he passed on his advice for dealing with Rodney McKay. He handed Mitchell a lemon, saying that McKay is fatally allergic to citrus, and works best under threat of impending death.
Soon afterwards, Sheppard's team found a man called Lucius that everyone in his world adored, but they found obnoxious. Strangely, Dr. Beckett took Lucius back to Atlantis and soon everyone in the city fell under Lucius' charm. John revisited Lucius' planet and discovered he was using some kind of drug that makes the user generate a kind of pheremone that makes people want to please him. Having a cold, John himself was immune to it, but for that he was distrusted by everyone else, especially by Lucius who put him in a cell. John escaped and captured Beckett, who then created an antidote for the drug. John kept Lucius in a Jumper away from Atlantis while Beckett innoculated everyone on the city. After returning Lucius to his planet, John suddenly turned to Rodney and said "Hey, buddy, I'd better get back and clean your quarters before the next scout." before trotting away, making it obvious that McKay took some of the drug himself. Weir, Beckett, Teyla and Ronon immediately told Rodney to burn it all. John's reaction to this was not shown.
John was later captured by Acastus Kolya, who wanted to exchange him for new Genii leader Ladon Radim. Kolya tortured Sheppard by allowing a starved Wraith to feed upon him. John later made a deal with the Wraith to escape. The Wraith initially drained him, but later, keeping his word, gave him the "Gift of Life" which is typically reserved for devout Wraith worshippers and "Brother" Wraith, returning him to his correct age and health. John repaid the Wraith by returning him to a Wraith occupied world so he can return home. Sheppard also sent a warning to Kolya: if they ever met again, Sheppard would kill him on sight.
While testing a new "Gate bridge" that McKay and Lt. Colonel Samantha Carter came up with to accelerate transportation between Pegasus and the Milky Way, an Ancient ship was located, filled with living Ancients who reclaim Atlantis. With the expedition disbanded, Sheppard is assigned as the leader of an SG team. When General O'Neill sends a message to Stargate Command telling them that the Asurans have take control of Atlantis, Sheppard, Weir, McKay and Beckett hijack a puddle jumper and attempt to rescue O'Neill, Richard Woolsey, and Atlantis.
Alternate timelines
There are two known alternate-timeline versions of Sheppard:
In the episode "Before I Sleep", John Sheppard piloted the timeship that brought the alternate Weir ten thousand years into the past, and was accidentally responsible for the timeshift. He and Dr. Zelenka died after the ship crashed in the ocean near Atlantis due to an attack by a Wraith Dart. Only Weir survived.
In the episode McKay and Mrs. Miller, the alternate Rodney McKay known as "Rod" describes how the Sheppard in his universe is a member of Mensa and a know-it-all who makes the main timeline's Dr. McKay look humble in comparison. He came up with the plan to send Rod to "our" universe.
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, just seconds before that Atlantis rose to the surface. After a discussion with Dr. Weir, he 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. 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.
Aside from being the ranking military officer, Sheppard lead an exploration team that consisted of Dr. Rodney McKay, Lt. Aiden Ford and Teyla Emmagan. Sheppard's relaxed commanding style often put him at odds with his more by the book chief of security, Sgt. Bates, until a beating by a Wraith forced Bates to return to Earth.
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 did not fall into the trap.
Major SheppardOn a later mission, Sheppard was bitten by an Iratus bug 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 turned out to be 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.
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 shield, 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 Kolya survived, when he captured them while they were trying to find the location of a ZPM. While trying to solve a puzzle, Sheppard revealed that he took the Mensa exam and, though it is implied that he passed (he solved a complex puzzle by recognizing it from the Mensa test), his results have never been revealed.
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 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 bombs 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.
Season 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 and shot him with a Wraith stunner but was unable to stop him, and Ford fled through the Stargate.
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 Oversight 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.
Season Two
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 they had to transport 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 another system reset still failed to clear the virus, Sheppard deduced that the virus was using the hard drive of the F-302 he was beamed out of earlier, which has been tailing them. He took the stripped F-302 out, with McKay in the back seat, and managed to destroy the infected fighter after some fancy flying.
Soon thereafter, Major Lorne's team discovered Lt. Ford's whereabouts. When they arrived 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. Ronon returned to Atlantis with them and, after seeing him sweep the floor with the Marines and pass the shooting range without even blinking, Sheppard offered him a place on his team.
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.
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, did not feed on humans, as she had been raised by a human herbologist as his own daughter. 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. 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.
Sheppard was confined to his rooms but, when Dr. Weir visited him, the heavily-mutated Sheppard attacked her and escaped. After a chase, Ronon finally stopped him; Sheppard was then returned to the infirmary, restrained, and sedated while the team continued to research a cure. Dr. Beckett deduced that Iratus 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 a team 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.
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 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 did not believe him. Meanwhile, Teyla discovered that a Wraith had infiltrated the VR system. Sheppard was finally able to convince the captain of the Aurora of the truth of their situation, but the Wraith infiltrator had succeeded in destroying the intelligence data. As two Wraith cruisers were on their way to intercept the ship, the captain gave Sheppard the ship's auto-destruct code. Once safely onboard the Daedaulus, the Aurora exploded, destroying the Wraith cruisers.
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, 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 did not 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, but the interrogation was interrupted by the emergence of a second hive ship from hyperspace before she could get any information out of him. Sheppard and his teammates managed to escape their cell, freeing a captured woman, Neera, from a cocoon on the way, but they were then recaptured. Sheppard and Neera were placed in a cell together, 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.
Soon after, while looking for the source of an energy spike, they found a cave whose entrance was protected by a kind of force field. 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 did not last long and some days later, angry and hungry, he decided to move away from the cave. He got hurt while saving a man, Avrid, from a strange energy Beast. He woke up in Avrid's home being cared for by his sisters, Teer and Hedda, and he learned all the people in the Sanctuary were working for Ascension and that there was no way out. Six months passed for him before the rest of his team, plus Beckett and Weir, arrived, but it only have been a couple of hours for them, since Sanctuary was really a time dilation field constructed by the Ancients to help people looking for Ascension. The Beast was a manifestation of the Cloister's people fears and Sheppard's example finally prompted them to confront it. Once vanquished, they were able to finally Ascend. Teer offered John to accompany them, but he refused. She told him, however, that they will keep the time dilation field open until they left.
When an accident trapped Dr. McKay underwater in a broken Puddlejumper, Col. Sheppard and Dr. Zelenka took another Puddle Jumper down to help him. Sheppard convinced Zelenka to change the Jumper's cloak into a shield that would allow them to stand the high underwater pressions. The mission was a success and they rescued McKay safely.
When Michael, the Wraith turned human turned Wraith again, approached Atlantis with an offer of information in exchange of Dr. Beckett's retrovirus, Atlantis reluctantly agreed. It turned out to be a trap, and Sheppard was forced again to pilot a F-302 against a hive ship. When the two hive ships went into hyperspace, John disappeared with them.
Season 3
John managed to use the 302 docking clamps to attach himself to a Hive ship. With Michael's help, he damaged the hive ship's hyperspace engines and boarded it to rescue McKay and Ronon. They boarded a Wraith transport and communicated with the Daedalus, which beamed them onboard. The Daedalus was severely damaged, however, and they were forced to use Dr. Beckett's retrovirus to turn the Wraith into humans and take over their hive ship.
They used the hive ship to get back to Atlantis and decided to settle the amnesiac former Wraith into an uninhabited planet. When they returned to the planet, they discovered that some of the humans were turning back into Wraith and he ordered McKay to fire on the planet, using the Hive ship's energy weapons to destroy them. They were forced into battle by another hive ship, and theirs was destroyed (it is not clear what happened to the other ship), but they managed to save themselves using a Puddle jumper, and they were rescued by the Daedalus.
When Sheppard met Cameron Mitchell of SG-1, he passed on his advice for dealing with Rodney McKay. He handed Mitchell a lemon, saying that McKay is fatally allergic to citrus, and works best under threat of impending death.
Soon afterwards, Sheppard's team found a man called Lucius that everyone in his world adored, but they found obnoxious. Strangely, Dr. Beckett took Lucius back to Atlantis and soon everyone in the city fell under Lucius' charm. John revisited Lucius' planet and discovered he was using some kind of drug that makes the user generate a kind of pheremone that makes people want to please him. Having a cold, John himself was immune to it, but for that he was distrusted by everyone else, especially by Lucius who put him in a cell. John escaped and captured Beckett, who then created an antidote for the drug. John kept Lucius in a Jumper away from Atlantis while Beckett innoculated everyone on the city. After returning Lucius to his planet, John suddenly turned to Rodney and said "Hey, buddy, I'd better get back and clean your quarters before the next scout." before trotting away, making it obvious that McKay took some of the drug himself. Weir, Beckett, Teyla and Ronon immediately told Rodney to burn it all. John's reaction to this was not shown.
John was later captured by Acastus Kolya, who wanted to exchange him for new Genii leader Ladon Radim. Kolya tortured Sheppard by allowing a starved Wraith to feed upon him. John later made a deal with the Wraith to escape. The Wraith initially drained him, but later, keeping his word, gave him the "Gift of Life" which is typically reserved for devout Wraith worshippers and "Brother" Wraith, returning him to his correct age and health. John repaid the Wraith by returning him to a Wraith occupied world so he can return home. Sheppard also sent a warning to Kolya: if they ever met again, Sheppard would kill him on sight.
While testing a new "Gate bridge" that McKay and Lt. Colonel Samantha Carter came up with to accelerate transportation between Pegasus and the Milky Way, an Ancient ship was located, filled with living Ancients who reclaim Atlantis. With the expedition disbanded, Sheppard is assigned as the leader of an SG team. When General O'Neill sends a message to Stargate Command telling them that the Asurans have take control of Atlantis, Sheppard, Weir, McKay and Beckett hijack a puddle jumper and attempt to rescue O'Neill, Richard Woolsey, and Atlantis.
Alternate timelines
There are two known alternate-timeline versions of Sheppard:
In the episode "Before I Sleep", John Sheppard piloted the timeship that brought the alternate Weir ten thousand years into the past, and was accidentally responsible for the timeshift. He and Dr. Zelenka died after the ship crashed in the ocean near Atlantis due to an attack by a Wraith Dart. Only Weir survived.
In the episode McKay and Mrs. Miller, the alternate Rodney McKay known as "Rod" describes how the Sheppard in his universe is a member of Mensa and a know-it-all who makes the main timeline's Dr. McKay look humble in comparison. He came up with the plan to send Rod to "our" universe.