The year is 2075. Instead of a bright and peaceful future, human civilization is in a state of polluted, dilapidated ruin akin to post-World War II Europe. A corrupt mega-corporation, Grathius Inc., controls the world by force, using pacification squads to kill any who oppose them.

The game's protagonist is Flynn Haskell, the leader of a small band of terrorists/resistance-fighters determined to rid the world of Grathius and their evil schemes. Later the player meets up with a female scientist Eve whom Flynn regards as the best helper he could get. Flynn, while exploring once, is captured and put into jail but successfully escapes with another resistance member named Duffy who also helps him in his next destination Urbia, as she is familiar with their resistance leader Tara.

The game's main plot revolves around a new technology developed by Grathius, nano-machinery based cloning, that allows the corporation to clone its fallen troops and gives them an unstoppable immortal army. As the game progresses, the player travels from San Francisco to Taiwan to Japan, recruiting new characters into the resistance and capturing Grathius cloning devices for their own personal use.