The player takes on the part of Prisoner 849, an otherwise anonymous person aboard the prison spacecraft Vortex Rikers. The ship was under way to a prison moon, but was pulled to an uncharted planet before reaching its destination. The ship crash-lands on the lip of a canyon on the planet Na Pali, home of the Nali, a primitive tribal race of four-armed humanoids.
The Nali and their planet have been subjugated by the Skaarj, a race of brutish yet technologically advanced reptilian humanoids. Skaarj troops board the downed Vortex Rikers and kill the remaining survivors, save for Prisoner 849, who manages to find a weapon and escape from the ship.