In the alternate future of Prey, President Kennedy survives the assassination, which sets off a turn of events leading to the central conflict. After recovering from the attempt on his life, Kennedy threw his nation further into the space race by taking control of a U.S./Russian joint program and transforming a Russian satellite into a fully functional R&D facility meant to study non-terrestrials. This facility later became Talos I, a highly advanced space station owned by the TranStar Corporation.

After awakening on Talos I, Morgan finds the station overrun by a previously contained non-terrestrial entity called Typhon, which the scientists had been studying and using to improve the scope of human abilities. Aided by strange alien-based powers, Morgan must survive the incursion, uncover the mysteries surrounding the Typhon and save humanity from the impending danger aboard the station.