William was born to a man who had strong negative opinions about working for the American government and about Nicholas Ballard and his grandson. William eventually went to Cambridge University for graduate school where he was classmates with Doctor Radek Zelenka. Due to his own strong opinions about US policy and how he didn't think one should aid it in any way, William had an argument in which he said nasty things to Zelenka when he discovered that he was going to work for the American government. Despite his views, William eventually went to work for the SGC as an archeologist under Doctor Daniel Jackson. (SGA: "Allegiance")
William proposes performing a systematic survey of the contemporary technologies the cultures encountered by the Atlantis expedition in the Pegasus Galaxy possessed with an eye to helping their allies taking the next steps in their development. William's plan is eventually approved and he is sent to Atlantis on the Daedalus's second trip to the Ancient city following its return to Pegasus. However, before William's departure, the situation in Atlantis changes with the city landing on a frozen planet with nearly-depleted ZPMs and is thus far more vulnerable to Wraith attack than when William proposed his idea. Though William has second thoughts, he ultimately embarks aboard the Daedalus with the second phase of his project becoming more important due to the threat from Queen Death.
While aboard the Daedalus waiting to arrive in Atlantis, William eats lunch with Lt. Colonel Melissa Hocken, the commander of the Daedalus F-302 wing. The two briefly joke about William's job and a comparison to Doctor Daniel Jackson before they are joined by Jeannie Miller, something that makes it awkward for all three of them due to the kidnapping of Jeannie's brother Doctor Rodney McKay being the reason for her going to Atlantis in the first place. After a few awkward minutes of William and Mel trying to find something to say, Jeannie leaves, causing the two to acknowledge the awkwardness.
After arriving in Atlantis, William visits the mess hall for some food and encounters Doctor Eva Robinson who he had known at the SGC. As the two joke about Atlantis' architecture, they are joined by Doctor Radek Zelenka who is still angry at William for the comments he'd made the last time they'd met about working for the American government and then going to work for them himself. The two briefly argue through Eva before she stops them and William admits that while he didn't know Zelenka was in Atlantis and still would've come if he had known, he would've at least sent Zelenka an email so William didn't catch him by surprise. When Zelenka is suddenly called away, William agrees with Eva that whatever it was isn't good at all.
After Ronon Dex notices that the Satedan City Museum is still relatively intact, Zelenka asks to have William accompany the team exploring the museum because, as an archeologist, William is best suited to the search. After Teyla is able to make a deal with the Satedan leader Ushan Cai, William, Zelenka, Teyla and Ronon make their way through the ruins of the Satedan capital city to the museum. Along the way, William takes interest in the ruins around them and is sympathetic to Zelenka's story about the aftermath of World War II for the Czech Republic and how he sees it to be similar to the situation on Sateda.
Once inside the museum, William is disgusted at the bird droppings at the base of a column and has his interest drawn by the murals in the museum's Hall of the Ancients, causing William to express a desire to have Ronon teach him his language so he can read them. After they unexpectedly find supplies in the room, William surprises the others by being able to read the Genii language and thus learning that its their version of an MRE that has been recently left. As Ronon and Teyla go to scout for the Genii, William and Zelenka stay behind. Due to the time constraint, Zelenka orders William to look through the hall for anything they can use on Atlantis, particularly undamaged control crystals. William quickly finds some useful crystals and decides to make a list of everything he can find so that they can see what they have and take what they need with the most useful things first.
Together the two find many useful things, too many for them to be able to carry back to Atlantis. After hearing Zelenka swear in Czech while exploring the collapsed portion of the room, William investigates to find that Zelenka has found an important looking intact crystal. Zelenka tells William that no matter what, the crystal must get back to Atlantis as its a control crystal for the stardrive of a city-ship, something they can use to make Atlantis fly again if they can find a ZPM as the control crystal in Atlantis burned out upon their arrival in the Pegasus Galaxy. Hearing approaching footsteps, the two men quickly hide in a small storage room hidden within the debris where they both ready their weapons in case they are discovered. The two listen as the Genii discuss the evidence of other people being there, causing both men to swear as they realize that they didn't bother to cover their tracks. Once the Genii leave, Zelenka returns to the hall while William covers him. As Zelenka converses with Teyla on the radio, William finds what he suspects to be part of the museum's catalogue in the form of plates in the storage room and takes it.
Carrying the hyperdrive control crystal, they return to the Gate square where Ronon orders William and Zelenka to dial out to New Athos and take the crystal there until they can dial Atlantis. After Zelenka convinces Ronon and Teyla to let him stay while they talk with Cai, William is sent on alone with orders to tell Lt. Colonel John Sheppard that Ronon and Teyla will check in with him in an hour and if he doesn't hear anything, to send the cavalry. Although William protests at first, he agrees after Zelenka reiterates the importance of getting the control crystal back to Atlantis.
After returning to Atlantis, William enlists the help of an airman from photo recon to scan the information on the plates into a computer so they can have a better idea of what might be in the museum. As they scan the information in, William and the airman spot a drawing of what appears to be a ZPM on the final plate. William orders the airman to clean the image up while he contacts Ronon to translate the notes accompanying the image, deciding not to tell Zelenka until they are sure there's actually a ZPM in the museum. Figuring that Ronon will take awhile, William heads to the mess hall for coffee where he meets up with Ronon who is already there and accompanies William back to the lab where he is working on the plates. There, they find Zelenka who learned of what's going on after calling the airman for a progress report. Zelenka and William briefly argue about William not calling Zelenka before Ronon interrupts them to explain that the notes describe a ZPM that was found by a museum curator and was moved to a more secure storage thirty years before.
After Sheppard agrees to try to help the Satedans find a diplomatic solution with the Genii, William accompanies the team that goes back to tell Cai and helps to explain about the ZPM to Cai and how it is likely intact since the curators would've likely taken precautions to protect it. William also suggests that they have Atlantis engineers help the Satedans gain hydroelectric power and is disappointed when Cai refuses to let them look through the museum again.
When Atlantis sends a delegation to negotiate with the Genii on Sateda, William attaches himself to it without asking for permission, telling Zelenka that as an archeologist, he could be useful despite Zelenka reminding William of how many times he's argued that he's not an anthropologist. On Sateda, William's interest is drawn by the meaning of the Genii uniforms and the behavior of Sora Tyrus which leads to Zelenka explaining to him how Teyla was indirectly responsible for the death of Sora's father, something that she hasn't yet forgiven. Along with all but Sheppard and Colonel Steven Caldwell, William observes the opening of the negotiations from a distance and recognizes Ladon Radim's obvious attempts to derail the talks. As the three leaders argue, William recognizes that they are facing a long day.
Following the successful talks, the Atlantis expedition is given permission to search the museum for the ZPM though William is left perplexed by how quickly the Genii conceded to a trade deal. After clearing a safe passage is created into the storage areas, William volunteers to be the one to go due to his job as an archeologist making him the best choice. William is lowered into the lower levels of the museum where he finds signs that the museum personnel had tried to move the most important pieces during the Wraith attack which destroyed most of the crates they left in the room William is lowered into. Looking around, William finds the passage he needs to go through mostly blocked, but with a small gap. Unsure of whether to go through it, William asks for Zelenka's advice, causing Zelenka and Ronon to join him. After Radek determines that it is stable, William squirms his way through the small gap into the room where the ZPM is supposed to be located. However, in the room, William finds most of the shelves empty and what hadn't been taken away, destroyed on the floor. William informs Zelenka of the bad news and continues futilely searching the room until he finds the body of a female soldier holding a case containing the intact ZPM. William manages to get the case through the gap to Zelenka who is able to determine that the ZPM is not at full power, but nothing more than that. William takes a picture of the skeleton and takes the slevee cuff for Ronon so that the Satedans will have a clue about who she was. After emerging from the museum, Zelenka informs William that while the ZPM has power, it is too minimal for more than possibly powering the shield for a few minutes or firing a few drones.
A few days later, William is working at a console in the Control Room going through the Atlantis database, a job at which William had made himself indispensable, when a Wraith cruiser and then a hive ship is detected exiting from hyperspace. In light of the threat, William quickly moves away from the console so the defense team can get at it. (SGA: "Allegiance")