Shortly after the arriving in Atlantis, he and Dr. Rodney McKay tested the Personal shield emitter by shooting McKay and shoving him off a balcony. That night, he told the Athosian children a scary story that was just the movie Friday the 13th and then showed Teyla Emmagan a recording of a football game. Later when Jinto went missing, Sheppard and Halling searched for him. They discovered the Atlantis transporter and found Jinto in a lab with the Containment vessel for the Shadow creature. Sheppard tried to lure it back inside the vessel but it would not reenter. Eventually, they allowed the creature to go through the Stargate to M4X-337. On a mission back to the Wraith homeworld, the team was attacked by Wraith warriors. He ordered a retreat but he was attacked by an Iratus bug and was fed upon. The rest of the team got him in the Puddle Jumper but on the way back to Atlantis the Jumper got lodged in the Stargate. After using salt and iodine to try to remove the Iratus bug, Dr. Carson Beckett suggested the use of a Defibrillator to stop his heart. After the bug released it's grip, he was then placed in the Event horizon until Dr. Rodney McKay freed the Jumper and he was revived on Atlantis. When his team encountered the Wraith for the fifth time in nine missions, Dr. Elizabeth Weir concluded there must be a spy in the city. Weir set up new security protocols that restricted the movement of the Athosians despite his objections. While on a Puddle Jumper exploration of Lantea with Lt. Aiden Ford, they discovered the mainland. After the Athosians relocated to the mainland, he and his team traveled to an unnamed planet. While deciphering ruins, he sent Teyla Emmagan and Ford to find the inhabitants to help with the translation. While they were away the Wraith attacked the ruins and he was shot with a Wraith stunner. Dr. Rodney McKay and Sgt. Stackhouse were able to drag him through the Stargate back to Atlantis but they were forced to leave Teyla and Ford behind. He became angry when Sgt. Bates accused Teyla of being the spy and was surprised when McKay found the Wraith relay device in her possession. It had been activated by Sheppard's Ancient Technology Activation gene gene when on Athos, and he had returned the lost 'necklace' to Teyla neither aware of what had occurred. He then used the device to lure the Wraith back to the planet and he and the team were able to capture a Wraith that he named Steve. When his team's Puddle Jumper crashed on M7G-677, he stayed in the village with Teyla Emmagan while Dr. Rodney McKay and Lt. Aiden Ford searched for the Electromagnetic field generator the Ancients left on the planet. He also attempted to convince Keras to not go ahead with the sacrifice. When Ford and McKay unplugged the Zero Point Module and a Wraith relay device activated, he destroyed the device but the villagers became angry for desecrating their shrine. Teyla was able to convince the villagers not to kill Sheppard for destroying it but Aries forced them to leave the planet. When the Wraith sent a probe, Ford and Sheppard attempted to shoot it down but failed. Fortunately, McKay was able to reactivate the device and the probe shut down. On a mission to Hoff, Chancellor Druhin showed his team a drug that they hoped would make them immune to Wraith feeding. He offered Dr. Carson Beckett's assistance in perfecting the drug. When Beckett reached the point where the drug required human testing, he convinced Dr. Elizabeth Weir to allow them to test it on Steve. After the test of the drug killed Steve, he warned Druhin that the Wraith would exterminate them when a single Wraith dies from the drug. Druhin refused and began administering it to the population. When half the people that received the drug fell ill and died, he took his team back to Atlantis. When the Atlantis expedition was running low on food, Teyla Emmagan brought he and his team to the Genii homeworld and introduced them to Tyrus and his daughter Sora Tyrus. After meeting with Cowen and coming to an agreement on trading C-4 and medical supplies for food, Teyla and Lt. Aiden Ford stayed for the harvest ceremony while he and Dr. Rodney McKay returned to Atlantis to discuss the trade deal with Dr. Elizabeth Weir. When he and McKay returned and found a secret Underground Bunker, they were arrested and Teyla and Ford were brought inside. Cowen revealed that the Genii Confederation used to span many worlds but was forced to hide in the bunker and pose as simple farmers to fool the Wraith. When Cowen revealed their plan to use the C-4 to complete their nuclear weapons, he offered McKay's help in speeding up their completion. After a loose alliance was formed between the two, he and his team joined Cowen and Tyrus on a mission to a Wraith Hive ship. Once on the Hive, he, McKay and Cowen infiltrated a room with a data core and they download information to the Wraith data storage device. They returned to the Puddle Jumper and returned to the Genii homeworld. When they landed, Cowen tried to double-cross them and he drew his weapon but was not forced to fire as Cowen surrendered when two Jumpers decloaked. Upon returning to Atlantis, Dr. Peter Grodin analyzed the data on the device and discovered there were at least 60 Hive ships in the Pegasus galaxy. After the discovery of M5S-224's powerful atmosphere, he traveled to Earth with Teyla Emmagan to brief Stargate Command on the situation in the Pegasus galaxy. After the briefing, Sheppard took Teyla shopping and began to notice something was wrong. He instructed the driver assigned to him to take them to the apartment of his dreams. After they arrived and some of his deceased friends began to arrive, he knew something was wrong and shot one of them to see if they were real. Fortunately, this was all an illusion created by the inhabitants of the planet and he never left Pegasus. During a trip to the mainland with Teyla Emmagan, they discovered a storm approaching Atlantis. He and Lt. Aiden Ford traveled to Manara to negotiate with Smeadon about evacuating the Atlantis expedition there. After Dr. Rodney McKay and Dr. Radek Zelenka came up with a plan to use lightning to power Atlantis' shield and nonessential personnel were evacuated, he uncoupled one of the four Grounding stations and headed for the fourth when a Genii strike force under Acastus Kolya gated to Atlantis. After McKay was able to activate the radio and inform him that the Genii were after the C-4, he was able to get to the armory first and hide it. After McKay was tortured into revealing his plan to save the city, Kolya contacted him and demanded he uncouple the last grounding station or he would kill Dr. Elizabeth Weir. When he reached the grounding station, he was ambushed by two Genii soldier but was able to kill them with help from his Life signs detector. After contacting Kolya and informing him of the failure of his men, Kolya lied and said he killed Weir. After avoiding an ambush from three Genii soldiers, he disabled the Naquadah generator that powers Stargate Operations and infiltrated it. After knocking Ladon Radim unconscious, he activated the Stargate shield killing fifty-five Genii soldiers when they attempted to send reinforcements through the Stargate. After retreating from Stargate Operations, he was contacted by Kolya and he demanded he reactivate the generators or he would kill McKay and Weir. While reactivating one of the generators, he was captured by two Genii soldiers but was saved by Teyla, Ford and Dr. Carson Beckett who returned from the mainland. They planed to attack Stargate Operations together and he sent Teyla and Beckett to fly a Puddle Jumper into the room to create a distraction while he and Ford went in on foot. The Genii eventually decided to retreat, trying to take Weir and McKay with them so he was forced to attack before the Jumper was in the room. McKay got away and Sheppard was able to save Weir by hitting Kolya in the shoulder. McKay is then able to raise the shield and save the city from the tidal wave. When Dr. Brendan Gall located the last remaining Lagrangian Point satellite, he along with a team of Gall, Dr. Rodney McKay and Dr. Abrams went on a mission in a Puddle Jumper to investigate. When they arrived, they detected a distress call from a near by planet. Once they got clearance from Dr. Elizabeth Weir, they landed on the planet and headed for the Wraith supply ship. Once inside the ship, they discovered several Wraith warriors that had been fed upon. After splitting up to search the ship, McKay realized that the cocoons could keep Humans alive indefinitely if they had a large enough power source and there could still be survivors. He radioed Gall and Abrams and ordered them to fall back to the Jumper. On the way back, Gall and Abrams are attacked by a Wraith survivor. It fed on Abrams and took Gall. He and McKay came on Abrams' body and took his weapons and found two Wraith grenades on a dead Wraith warrior. After hearing Gall scream, they were able to locate him but he had been fed upon but was still alive. He ordered McKay to stay with Gall while he went after the Wraith that was heading for the Jumper. When he caught up to the Wraith, it had already made it to the Jumper. After luring the Wraith into the open, he shot him several times with his P90 but the Wraith healed itself and grabbed a Beretta from the Jumper and shot him in the arm and disabled his P90. After bandaging his arm, he used a flare to lure the Wraith out of the Jumper and tried to enter it but the Wraith protected it with a shield. He then used one of the grenades as a mine but the Wraith survived and he fired on him with his sidearm until he was out of ammo. The Wraith was about to feed on him when McKay arrived and fired on him with his sidearm. When Lt. Aiden Ford and Teyla Emmagan arrived in orbit above the planet in a Jumper, he used a energy bar to attract the Light bugs to the Wraith and ordered them to fire a Drone weapon at the largest life signs reading killing the Wraith. On a mission to Doranda, the team discovers an Ancient outpost. While Teyla Emmagan and Ronon Dex embarked on a trading mission to Belkan, he and Dr. Rodney McKay worked on the outpost to perfect Project Arcturus. After several failed simulations, McKay believed he had perfected the containment field and they prepared for a test. During the test, the field began to fail and McKay sent Dr. Collins to adjust the field manually. The field partially collapsed and Collins was killed form radiation poisoning. After returning to Atlantis, Dr. Elizabeth Weir shut down the project. Later, McKay was able to convince him to talk to Weir about allowing the two of them to return and restart the project. During the first test at half power, the device overloaded and McKay was unable to shut it down. The device then began releasing energy by discharging the weapon at the wreckage in orbit to prevent a catastrophic overload. Unable to prevent a full overload, they evacuated to the Puddle Jumper and had to avoid the weapons fire. Luckily, the Daedalus arrived and provided cover for their escape through the Stargate before the overload resulted in the destruction of 5/6th of the solar system. Back on Atlantis, McKay apologized but he told him it may take time for him to trust him again.On a mission to an unnamed planet, he learned that the villagers were being terrorized by what they call the Daimos. Their description of it is very similar to that of a Wraith. Ronon Dex offered his help in killing it but he ordered him to wait until morning and the whole team would go. The next day, Ronon successfully tracks a female Wraith into a cave. The team chases her inside but she hides behind a man named Zaddik. Zaddik explains that her name is Ellia and she does not feed because of a serum he created. He returned to Atlantis and explained the situation to Dr. Elizabeth Weir and Dr. Carson Beckett who volunteered to come to the planet to examine the serum and Ellia in the hope of perfecting his retrovirus. Once back in the cave, Teyla helped Ellia use her telepathic abilities to locate the adult Wraith that was killing the villagers. He, Teyla and Ronon left to kill it. When Ellia took Beckett's retrovirus and transformed into a creature closer to that of an Iratus bug, Teyla was knocked unconscious and Sheppard and Ronon were forced to kill her but not before she fed on Sheppard's arm. Back on Atlantis, Beckett noticed that Sheppard's wound had healed much faster than usual and that he was infected by the retrovirus. Sheppard later noticed that his former wound was slowly transforming him into a bug-like creature. Beckett attempted to slow it down by an inhibitor, but Sheppard was eventually transformed. Beckett came up with a plan to use Iratus bug embryonic stem cells to replace Sheppard's mutating cells. The team lead by Major Evan Lorne first went to a planet with Iratus bugs but they were unable to get close enough to get any eggs without the bugs attacking. After Weir informed him of the situation, he escaped from his quarters. Several teams helped track him down and Ronon stunned him with his Particle magnum. The team was about to say goodbye to him, until Beckett realized that he had the pheromone to stop the bugs from attacking. He was able to get the eggs and was transformed back to Human again. He and his team traveled on the Daedalus to the Ancient ship Aurora. Since there was no life support they were forced to wear space suits when they beamed over. After Dr. Rodney McKay got life support functioning, he ordered Ronon Dex and Teyla Emmagan to search the ship and count the stasis pods. When McKay realized that the pods the crew was in was also a Virtual reality pod in addition to a stasis pod, he volunteered to enter one of the empty pods to contact the crew. After entering the virtual reality, he was arrested by one of the crew and taken to the Captain. He tried to explain that they are in stasis but the crew was unaware of their situation and placed him in the brig. He tried to convince First Officer Trebal to let him talk to the Captain again to convince him that Atlantis had been evacuated 10,000 years ago but she ignored his request. He then exited the pod and reentered in order to get the drop on the guard and escape. He cornered the Captain in his quarters and tried to explain but was shot by a Lantean stun weapon by Trebal and returned to the brig. After McKay entered the program and informed him that a Wraith was also in the program and two Wraith cruisers were on their way, he realized that the Wraith had to be First Officer Trebal. The two escaped from the brig and he went to the bridge to talk to the Captain again while McKay went to disconnect the Wraith. When he entered the bridge and told the Captain that Trebal was a Wraith, McKay was able to disconnect it and this proved the truth to the Captain. After the Captain gave him the self-destruct codes, he exited the pod just in time help McKay kill the Wraith. They set the self-destruct and beamed back to Daedalus before the Aurora blew and destroyed the cruisers. Back on Atlantis, he, his team, Dr. Elizabeth Weir and Colonel Steven Caldwell toasted the crew with Champagne. He and the team were taken by Lt. Aiden Ford's Coalition, to formulate a plan to destroy a Wraith Hive ship. Ronon Dex, Teyla Emmagan and Dr. Rodney McKay were dosed with the Wraith enzyme while he was kept clean in order to convince Dr. Elizabeth Weir that the enzyme was safe. After Ford explained the plan to use a Wraith Dart to plant C-4 on the Hive, he agreed to help but planned to use the Dart to dial Atlantis. After McKay fixed the Dart, Ford changed the plan and made McKay stay behind to ensure he kept his part of the bargain. He beamed everyone into the Dart and headed through the Stargate. While approaching the Hive the Dart went on Autopilot and forced Sheppard to unload his cargo blind. Most of Ford's men were beamed off a ledge. Believing Sheppard did it on purpose, Ford turned off his radio against Teyla's wishes. When Sheppard landed the alarms sounded and he was captured as were the others. Once in a cell the group managed to escape by using Ronon's knives to hit the door controls but they were quickly captured. The Wraith separated the team this time and put Sheppard in a cell with Ford and Neera, a girl they tried to rescue from a cocoon. While in the cell, Ford began to experience withdrawal and was taken by the Wraith Commander to a cocoon. After Neera attempted to get information from him, he realized she was a spy. He was then taken to see the Wraith Queen. While being questioned, he fooled the Queen into believing he was a Wraith worshipper for the Queen of the other Hive and was sent to kill her. Before the Queen could feed on him, Ford entered and shot her with Ronon's Particle magnum. While Ford drew the Wraith off, Sheppard freed Teyla and Ronon and beamed them into a Dart. After firing on the other Hive and forcing them to fight, Sheppard headed for the Spacegate and traveled to an uninhabited planet to release Ronon and Teyla. They then headed back to Atlantis.Sheppard came to Earth to operate the Ancient Control chair in an effort to defend Earth against the Wraith underling's ZPM powered hive ship at the Battle of the ZPM powered Hive Ship after being warned by Todd who had ordered the ship's creation. 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. (ATL: "Enemy at the Gate")
He was one of the two pilots of Atlantis when it was returned to the Pegasus galaxy, and assisted in identifying the problem with the hyperdrive array on the east pier. This problem eventually caused Atlantis to drop out of hyperspace early, and meant Shepprard was forced to land the city on a new planet on the outskirts of the Pegasus galaxy. While on a mission to Manaria he released Todd (also known as Guide) back to his alliance to act as a counter to the rise of Queen Death to prominence among the Wraith.
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