Sheppard was hired by the Weyland Corporation to serve as a mechanic responsible for maintenance of the EVA suits aboard the USCSS Prometheus during its voyage to the distant moon LV-223. After spending two years in hypersleep, Sheppard along with the other crew members were awaken. As the Prometheus nearly arrives on LV-223, Vickers, Shaw and Holloway briefed the crew on their mission to find the Engineers. After the Prometheus crew's first expedition to the Engineer temple, he helped David retrieve Holloway and Shaw after they are trapped by the Silica storm outside the Prometheus. He stood by one of the ship's airlocks helping Holloway and Shaw board the vessel when David finally rescues them.
Sheppard along with Jackson, Vladimir and Taplow later attempted to kill Fifield who has been mutated by the black liquid and was running rampant at their ship's hangar bay by shooting him multiple times with pistols, but the mutated Fifield proves to be too agile, fast and resilient. Sheppard and Jackson then escaped into one of the RT-01 vehicle and helped killing Fifield by running him over twice with Janek finishing the mutant off using the the flamethrower. The shocked Sheppard then proceeded to drive the RT-01 Transport vehicle out of the hanger on to the plains of LV-223 only to be never seen again. His fate remains unknown.