XO (Second officers)
2004 - 2005
In 2004, Stargate Command launched a new team of individuals who headed to the Pegasus galaxy after Dr. Daniel Jackson uncovered the address for Atlantis, the Lost City of the Ancients. Dr. Elizabeth Weir, a former head of Stargate Command was put in charge of the expedition alongside Colonel Marshall Sumner who was the Military Officer. The expedition itself with new member Major John Sheppard later arrived in Atlantis and began settling into their home until Dr. Rodney McKay realized that the city had been submerged underwater and that the last Zero Point Module or ZPM was keeping the city's shields up, thus preventing the city from being overrun by the ocean.
Realizing time was of the essence, Weir ordered Sumner and his team to go off-world and try to find a new power source. They arrived at a planet called Athos and met the leader of the Athosians, a young woman named Teyla Emmagan where she told them about the Wraith, enemies of the Ancients and begged them to return to their world so that the Wraith would not learn of their existence. Eventually, the Wraith attacked Athos, capturing Teyla, Sumner and a few of the soldiers including Sgt. Bates. Sheppard and Lt. Aiden Ford returned to Atlantis, bringing with them the Athosian refugees who had survived the attack on their home planet.
In the process, Atlantis later rose to the surface, meaning that the city was finally free of the ocean but had no shields to protect itself if it came under attack from any enemies.
Sheppard later led a rescue team and saved Teyla and Bates as well as the captured Athosians but during the battle he was forced to kill Sumner as he had begun aging rapidly due to the Wraith Keeper feeding on him. They all later returned to Atlantis where in the aftermath of Sumner's demise, Sheppard became the ranking Military Officer for Atlantis and was later told that he had to begin choosing members of his new team which later became known as AR-1 and was composed of himself, Teyla, Ford and McKay. (ATL: "Rising")
During a routine mission, Sheppard was attacked by an Iratus bug which began feeding of his life force but thanks to the effects of Ford, the bug was later killed, saving Sheppard's life. On another mission, AR-1 headed to a planet called Hoff where they learned that the people there had developed a new drug which they hoped would prevent the Wraith from feeding off them. AR-1 later returned to the planet accompanied by Dr. Carson Beckett who later helped a Hoffan scientist named Perna put the finishing touches to the drug. After the trails were successful which involved a Wraith that AR-1 had captured feeding a human test subject, the Hoffans began mass-inoculation straightaway but it was later discovered that the drug itself had a side-effect: 50% of those who took it died while the other 50 survived. The Hoffans, realizing the success of the drug voted in favor of it and even asked AR-1 to help them bring the drug to other worlds but Sheppard told them that the Wraith would wipe them as a result and disgusted by the society's willingness to easily sacrifice its people withdrew his support and he and his team returned to Atlantis. AR-1 later came across a race known as the Genii who were not farmers but in fact a military society and would later become their greatest enemy. The Genii leader, Commander Cowen told a captive Sheppard and McKay that his people had been building A-bombs for years in hopes that they could be one day used to destroy the Wraith but any chance of a possible relationship between the two races was permanently soured when the Genii held Teyla personally responsible for leaving Tyrus behind on a Hive ship and as a result, the Atlantis expedition and Genii became sworn enemies. (ATL: "Thirty-Eight Minutes", "Poisoning the Well", "Underground")
The Genii later returned led by Cowen's henchman, Acastus Kolya who intended to take Atlantis during a huge storm that threatened to destroy it. Although most of the personnel had gone off-world including Beckett, Teyla and Ford, only Weir, McKay and Sheppard were left behind. Koyla invaded the city and took both Weir and McKay, forcing Sheppard into a game of cat and mouse as he attempted to rescue his two friends while preventing Atlantis's destruction. Sixty Genii soldiers were killed when Sheppard triggered the Stargate shield. Eventually, the Genii fled the city and the storm passed, sparing Atlantis. (ATL: "The Storm", "The Eye")
AR-1 met up with Koyla again on a remote planet called Dagan. Kolya had his men hold both Teyla and Ford hostage while ordering Sheppard and McKay to figure out the clues regarding the current position of a ZPM that both sides were searching for. However, they both lost in the end when the newly formed Brotherhood informed AR-1 that they were going to put the ZPM into hiding and wait for the Ancients to return so that they could be greatly rewarded, not realizing that the Ancients themselves were long gone. When AR-1 got back to Atlantis, they were informed that three Hive ships were on their way to attack Atlantis and would reach the city in less than two weeks. (SG1: "The Brotherhood")
Teyla later discovered that her ancestors had been experimented on by a Wraith which meant that she possessed Wraith DNA which gave her a unique ability and also meant that she was able to get inside one of the Hive ships. She later informed her fellow team-mates along with Beckett and Weir that the Wraith were heading for a new rich feeding ground: Earth. (ATL: "The Gift")
With time running out, Atlantis began preparing for a wave of assaults. Thanks to McKay's help, they managed to power up an Lagrangian Point satellite which caused the destruction of one Hive ship but the other two then turned on it and destroyed it, killing Dr. Peter Grodin who was on it. Forced into a corner, the remaining members were forced to bring the self-destruct online but as they headed for the Alpha Site, they received an incoming wormhole that was revealed to have come from Earth, meaning that the messages they had sent had gotten through to Stargate Command and Colonel Dillon Everett came through along with Marines. Taking over the control of Atlantis, Everett informed Weir and the rest of the team that they were going to protect Atlantis at all costs. Preparations began straightaway for the defence of the city as Railguns were put up and mines were laid in space by several cloaked Puddle Jumpers but the mines were quickly destroyed by Asteroids that the Wraith had somehow managed to control, resulting in the sensors being disabled for hours due to the radiation. (ATL: "The Siege, Part 1", "The Siege, Part 2")
In an attempt to get some extra bombs, Weir went to the Genii who at first were unwilling to help but later changed their minds and sent two nuclear devices back with her. The devices were later discovered to be incomplete, forcing McKay and his second-in-command Dr. Radek Zelenka to finish them despite suffering from exhaustion. Realizing that the Hive ships needed to be attacked from the air, Sheppard volunteered himself for a suicide mission and approached them in a cloaked Jumper. (ATL: "The Siege, Part 2")
2006 - 2007
Major John Sheppard's mission worked, causing grave damage to the two Hive ships. He was later saved by the Daedalus before being taken back to Atlantis. While there, Colonel Steven Caldwell sent two of his men down to Atlantis, bringing with them a Zero Point Module for Dr. Rodney McKay and later took off, ordering his ship into battle against the two Wraith Hive ships. However the two Marines guarding McKay were later taken out by a Wraith but luckily, Teyla Emmagan arrived in the nick of time and the ZPM was brought online. Atlantis later faked an explosion, and was successful in tricking the Wraith into believing that they were dead.
Meanwhile, Lt. Aiden Ford was located just outside the city's shield, having been in the ocean for nearly an hour after being fed on. He managed to survive but Dr. Carson Beckett later discovered that the Wraith enzyme was in Ford's system. Having gone insane and developed an addiction to the enzyme, Ford later fled Atlantis for good. (ATL: "The Siege, Part 3")
While on the return journey to Atlantis, it was revealed that Sheppard had been promoted to Lt. Colonel. The Daedalus faced a huge battle when it was later found to have a Wraith computer virus on board, one that had probably been uploaded during the previous battle. After several efforts, it was finally destroyed for good and the ship managed to get to Atlantis safely. (ATL: "The Intruder")During their exploration of a planet, Dr. Parrish and Major Evan Lorne (now on assignment in the Pegasus Galaxy) uncovered a dead Wraith and brought their findings back to Atlantis. Beckett also revealed that the enzyme sac was removed, leading Sheppard to suspect that the missing Ford was responsible and he ordered a through-search of the planet as a result. Both he and Teyla were later captured by a mysterious man named Ronon Dex who explained that he was a Runner, a person implanted with a tracking device by the Wraith and then released to be hunted down. He later told Teyla that he had been on the run for seven years. Sheppard later made a deal with Ronon: In exchange for the tracking device being removed, Ronon agreed to help capture Ford. Beckett later arrived and was successful in bringing the device out although Ronon passed out. However, Ford managed to escape by running into a Wraith Dart's culling beam. After that, Ronon returned to Atlantis and learned that his home planet, Sateda had been destroyed by the Wraith. He eventually became a permanent resident of Atlantis and also joined AR-1, replacing the missing Aiden Ford. (ATL: "Runner")
Relations between McKay and Sheppard took a frosty turn following McKay's attempts to finish Project Arcturus. It later proved to be disastrous when it killed one of the scientists working under McKay and attempted to kill both AR-1 members too. Luckily, they managed to escape thanks to the Daedalus giving them enough time to get to the Stargate. Following that, three quarters (or as McKay correctly states 5/6th) of that solar-system were destroyed. (ATL: "Trinity")
Sheppard later became infected with the Iratus bug retrovirus after being attacked by a Wraith named Ellia who had mutated into a creature closer to a Iratus bug. He began transforming into a bug and later escaped his quarters, causing destruction whenever he went. Thankfully, Ronon managed to stun him. With Sheppard in a coma, Beckett explained that they needed to act fast or the retrovirus's effects on Sheppard's body would be permanent. Sheppard triumphed at getting the stem cells and was eventually cured, reverting to human a few weeks later. (ATL: "Instinct", "Conversion")
Ford, having gone rogue re-emerged and captured AR-1. He told them that he now had a group of people following him and they were all on the enzyme. Ford told them that he had brought them here for a mission which involved the use of C-4 that the Genii had and they were going to help him destroy a Hive ship. Teyla, Ronon and McKay were later exposed to the enzyme, leaving Sheppard clear-headed. However the mission to destroy the Hive ship was a failure from the beginning as many of Ford's men were killed and he along with Sheppard, Ronon and Teyla were taken prisoner. McKay, having been left behind managed to overpower his guards and return to Atlantis where he was forced to go through Wraith enzyme withdrawal to kick his habit. AR-1 later escaped but Ford's fate wasn't known although it was assumed that he had died after the Hive ship exploded. (ATL: "The Lost Boys", "The Hive")
Atlantis later learned that The Trust had one of its Goa'uld operatives plant a bomb there in an effort to destroy the city. The operative was later revealed to be Caldwell. He was later overpowered by Ronon and tasered by Sheppard. Caldwell gave up the code required and Atlantis was successful in stopping the bomb from going off. Following that, Caldwell returned to his original self and his relationship with Dr. Elizabeth Weir, Sheppard and the Atlantis staff greatly improved. (ATL: "Critical Mass")
In a sudden change, Atlantis itself became the battleground where both Sheppard and Weir became possessed by two rogue alien consciousnesses known as Thalan and Phoebus. The two weren't husband and wife as they had led everyone to believe. In fact, they were both psychotic warriors hellbent on killing each other over a war that had caused both their worlds to be destroyed a long time ago but despite their best efforts which put Atlantis and the lives of its residents in jeopardy, they both lost. Following that, both consciousnesses were expelled from the bodies of their grudging hosts with Sheppard and Weir returning to normal once again. (ATL: "The Long Goodbye")
The Genii later returned with Ladon Radim requesting Atlantis's help as he wished to stage a coup d'etat against Cowen in exchange for a Zero Point Module. Sheppard and McKay both led the assault team to the planet where Ladon was. In return, Ladon sent a few Genii citizens including his sister Dahlia Radim to Atlantis for treatment. It was later discovered that they all had been afflicted with terminal radiation poisoning. Sheppard led a raid on Ladon's compound. However, after stunning Landon's guards, they found out that the ZPM had long run out of power and as a result, they were all knocked unconscious by gas and then taken prisoner. Cowen later contacted Atlantis with a list of demands, one of which involved several Puddle Jumpers. However, Ladon revealed that he had actually been planning a coup all along and freed Sheppard and McKay as well as Lorne and his team who had been captured instead of being killed. They all escaped through the Stargate and at the same time, Landon triggered a bomb, killing Cowen and his men. He was then later told that all the people he had sent to Atlantis including his sister would be cured of the poisoning. With Cowen dead, Landon became the new Genii leader. (ATL: "Coup D'etat")
Atlantis later faced its great challenge of all in the form of Michael Kenmore, a Wraith who had been captured and then changed into a Human through use of the Iratus bug retrovirus. Unbeknown to everyone, Michael would later go on to become the biggest threat the Pegasus Galaxy had ever seen. After some intense digging, Michael finally learned the truth regarding his past and escaped from Atlantis, capturing Teyla in the process. Michael later returned to his Hive while Sheppard and Ronon managed to rescue Teyla. (ATL: "Michael")
AR-1 headed to a planet called Taranis which was under grave danger from a supervolcano and managed to save its people from destruction although the planet was left incapable of supporting human life for several centuries. AR-1 also later uncovered a Aurora-class battleship named the Orion although its original name was Hippaforalkus which they used to transport the Taranians to safety. McKay and a team of scientists later began work on the ship, hoping to fully repair the damage it had suffered. (ATL: "Inferno")
Michael Kenmore soon returned to Atlantis and claimed that that the Wraith were being divided by a civil war and said that they wanted to use Dr. Carson Beckett's retrovirus to turn their rivals into humans to feed upon. In return, Michael promised to turn over valuable technical information about their weapons and defenses. But the whole thing was a trap as McKay and Ronon were taken hostage while Dr. Radek Zelenka later uncovered a worm-like virus that had been uploaded into Atlantis's computers which meant that the Wraith had gained all of Atlantis's knowledge and could use it against them.
Sheppard later embarked on a mission of his own and managed to attach his F-302 fighter-interceptor to one of the Hive ships before they entered hyperspace. With his options limited, Sheppard found himself racing against time to find a way to disable the Hive ships before they got to the Milky Way galaxy. In the meantime, Weir asked Caldwell to launch the Daedalus and the Orion so that both ships could tackle the Hive ships head on. Caldwell later agreed and both ships left with Lorne having been put in charge of the Orion despite the ship not being battle ready at all. Weir herself was later recalled to Stargate Command and had a meeting with her superiors including Richard Woolsey who demanded answers in regards to the whole Wraith situation.
On the Hive ship, McKay and Ronon escaped their cocoons and embarked on a quest to damage many vital systems as possible on the ship before they were eventually recaptured once again. Sheppard attempted to contact them but found the Wraith Michael instead. Michael then revealed that he didn't completely transform back into a Wraith after escaping from Atlantis and as a result became an outcast among his brethren. He then offered to help Sheppard, knowing that his days as a Wraith were probably finished and that the Humans were his only hope of survival. He told Sheppard of the most vital places where damage could be inflicted by the firing of a missile and Sheppard went along with it.
However, Sheppard was captured and taken into custody on the Hive but managed to escape thanks to Michael's efforts and the two later met up with Ronon and McKay before escaping onto the Daedalus. A huge battle erupted between the Hive ships and the Daedalus and the Orion. However, the Orion was destroyed in the process but the people on board managed to get to safety.
The group soon took over one of the Hive ships by sending over cans containing Beckett's retrovirus and releasing it as gas. All the Wraith expect for the Queen were turned into humans with memories as to their previous lives being completely erased as a result. The Queen herself was then neutralized for good. (ATL: "Allies", "No Man's Land")
International Oversight Advisory Agent Richard Woolsey arrived in Atlantis, attempting to see if Weir was capable of maintaining her control of Atlantis. In the meantime, Sheppard and his team returned to Atlantis with the Human-form Wraith in stasis but McKay later explained that they couldn't be held in stasis permanently.
It was then decided to sent the human-form Wraith free on M8G-352 under the guise that they had been exposed to a viral outbreak. But all hell broke loose when they began remembering their past lives and planned to use the remaining Wraith who were still human as an offering to the approaching Hive ship. During the event, Michael took Beckett prisoner but he was eventually saved by Sheppard and Ronon. They then all agreed to destroy the campsite in hopes of preventing the Wraith from getting there but the Hive ship arrived and attacked them. The Daedalus then arrived and found no trace of Sheppard's team but it was soon revealed that the five of them had managed to survive and were hiding in a cloaked Puddle Jumper. Woolsey later told Weir that she deserved to stay in command of Atlantis. (ATL: "Misbegotten")
In the months following, Atlantis came under attack from the Asurans who were attempting to destroy Atlantis for good by using a Stargate-powered satellite that assaulted the shields. During an attempt to move the city, the satellite broke through and left Stargate Operations damaged, injuring those who were in the room at the time including Dr. Rodney McKay, Teyla Emmagan and Ronon Dex. Dr. Elizabeth Weir was the worst hit, falling down the steps which left her unconscious and suffering injuries which included brain damage and a few cracked ribs almost immediately. She later flatlined several times and Dr. Jennifer Keller told McKay that there was no hope for Weir unless the Asuran nanites that had been left in her body after she had been attacked by Niam were brought to life and they alone were probably capable of repairing the injuries. Sheppard and McKay clashed over the debate but the nanites were reactivated, helping Weir heal but at a cost: she became part Replicator. (ATL: "First Strike", "Adrift")
While Sheppard, McKay and Ronon successfully obtained a Zero Point Module from the Asurans, they lost Weir in the process who sacrificed herself to give them enough time to escape. Following that, Weir's position as Head of Atlantis was left vacant until Colonel Samantha Carter took up the role. (ATL: "Lifeline", "Reunion")
After that Dr. Rodney McKay had been infected by a parasite that put him in a Second Childhood. So AR-1 and Dr. Jennifer Keller and Jeannie Miller brought him to a planet where he could be himself for a day and say goodbye to their friends. But Keller managed to save Rodney and get rid of the parasite and save his life. (ATL: "The Shrine")
AR-1 were invited to a planet to discuss an alliance, but instead it was them kidnapped by a group of people and taken to another planet. There was prosecuted for the crime against the people of the Pegasus galaxy and Lt. Colonel John Sheppard faced trial and tried to defend his team and the Atlantis expedition. The people of the Coalition of Planets acknowledged that AR-1 were responsible for more than 2 million lives since it came to the Galaxy. The punishment for the trial was to cut all the expedition's trade relations with their allies in the galaxy. But the team was later pardoned innocent with the help of Richard Woolsey. (ATL: "Inquisition")
Todd told the AR-1 that his underling took over the ZPM powered hive ship and planned to bring it to Earth. AR-1 tried to stop the Hive ship before it left the Pegasus but failed and the Hive ship flew on to the Milky Way. Sheppard went to Earth to use the Control chair trying to stop the Hive ship, and while it took the rest of the team with Major Evan Lorne to go to the Hive ship through the Stargate on board. The team lost Ronon Dex during a fight but he was brought back to life by the Wraith underling who was then killed by AR-1. AR-1 used Sheppard's F-302 fighter-interceptors Nuclear warhead to blow up the Hive ship and AR-1 managed to escape through the Stargate to the Alpha Site and end the threat. Atlantis eventually managed to return to Earth, landing near the Golden Gate Bridge in San Francisco. (ATL: "Enemy at the Gate")
- In an alternate reality, the team investigated an alternate Daedalus. They arrived on the ship when they realized the ship was jumping to several alternate realities. They didn't find a solution to get back to their reality. They ran out of food and eventually starved to death. (ATL: "The Daedalus Variations")
- In an alternate timeline where Lt. Colonel John Sheppard was sent 48,000 years into the future, Michael Kenmore successfully took over the galaxy with his Hybrid army and destroyed the Wraith. The Atlantis team tried to stop him, but Richard Woolsey ordered all resources pulled back to protect Earth. Colonel Samantha Carter was killed in a battle with three of his Hive ships, Ronon Dex died destroying a Hybrid production facility with the help of Todd, and Dr. Jennifer Keller died from exposure to the Hoffan drug. Major General Evan Lorne became commander of Stargate Command and allowed Dr. Rodney McKay to use Atlantis to stop all this from happening. (ATL: "The Last Man")
- Saved a number of planets from Wraith Cullings by evacuating them to Atlantis or to other planets.
- Survived a Wraith Attack on the city with a total of 15 Wraith Hive ships and their escorts.
- Converted the Wraith Michael Kenmore into a human on several occasions.
- Saved an entire colony of people from a super-volcano by evacuating them to either the Daedalus or to the Orion, a severely damaged Ancient warship that was stored on the planet.
- With the addition of Dr. Elizabeth Weir and Dr. Carson Beckett successfully defeated the Asurans who had taken control of Atlantis from the crew of the Tria.
- Saving Earth from the Asurans and the Wraith threat.
- Successfully launched Atlantis from the surface of Lantea, flew it into hyperspace where, due to combination of power levels and damage, it dropped out of hyperspace prematurely. AR-1 then raided Asuras for a Zero Point Module to power up the city to reach its new home on M35-117.
- Defeated the Asurans with a fleet consisting of the Daedalus, the Apollo, several Wraith Hive ships and several Traveler Ships.
- Wraith homeworld
- Genii homeworld
|First Atlantis Reconnaissance Team|
|Current members||John Sheppard · Meredith Rodney McKay · Teyla Emmagan · Ronon Dex|
|Former members||Aiden Ford|