In the year 2087, a remnant of the U.S. Army called the Desert Rangers is based in the Southwestern United States following the global nuclear war of 1998. A team of Desert Rangers is assigned to investigate a series of disturbances in the nearby areas and, throughout the game, explores the remaining enclaves of human civilization, including a post-apocalyptic Las Vegas. The player's party begins with four characters, and through the course of the game can hold as many as seven characters by recruiting certain citizens and creatures of the wasteland to the player's cause.

Over the course of the game the player's party discovers evidence of a larger menace that threatens to exterminate what is left of the human kind in the game's region and eventually the world. The menace, a pre-war AI computer that is operating from a surviving military facility; Base Cochise, where it is constructing armies of killer machines and cybernetically modified humans with which it is attacking settlements. Its goal is to replace the current 'flawed' population with genetically pure specimens. With the help from a pre-war android named Max the player recovers the necessary technology and weapons in order to confront the computer at its base and stop it by making the base's nuclear reactor go critical.