The game follows FBI Special Agents Fox Mulder (voiced by David Duchovny) and Dana Scully (voiced by Gillian Anderson) as they travel to a small town in the Rocky Mountains to dig into the source of some strange and unexplained murders. Sightings of ghostly apparitions, zombies and hints of alien presence lead them on a chase for an "inhuman" killer.

During the course of the story, Mulder and Scully follow leads to a remote location in Russia and then discover, and search, a mysterious half-buried alien space ship. Players can play as Mulder or Scully as they attempt to prevent alien colonization of Earth.