Setting

The game takes place 30 years after mankind fought a devastating war against an enemy known as "The Shroud". Exactly who or what the Shroud are is never actually explained. At the end of the game they are shown to be hairless humans with corpse-white skin and highly advanced technology, although whether they are aliens, terrorists, mutants, or something else is never clearly revealed. Supposedly, the Shroud were vanquished 30 years ago, but their reappearance towards the end of the game shows that this is not true.

In the wake of the war, a large portion of the Earth is now an uncivilized wasteland known as "the Zone", inhabited by Scavengers, the violent descendants of prisoners and convicts who were released by the Shroud during the war. Human civilization is now controlled by a government known as the Alliance. According to the game manual, the Alliance mostly live in off-world colonies on other planets, but this is never shown or mentioned in the game.

Main plot

Jack Mason is a medic for the Alliance, tasked with transporting a cryogenically frozen woman named Karina from the maximum security prison "the Anvil" to Alliance headquarters. While flying over "the Zone", Mason's ship is shot down by a surface-to-air missile, crash-landing to Earth. Mason is accidentally infected with the mysterious transgenic virus Karina is carrying, who escapes in the chaos that follows as Scavengers arrive at the crash site attempting to capture her; the pilot, Stubbs, is killed in the fracas but Mason manages to outfight them. Mason suspects an unusual nature behind the Scavenger attack, as they were not known to possess surface-to-air missiles.

Although Karina is highly distrustful of Mason, her former captor, the two of them team up to evade the Scavengers. Mason observes that Karina possesses bizarre powers granted to her by the virus; when experiencing strong emotions, she involuntarily produces an explosive effect that creates mass destruction while leaving her unharmed. Mason and Karina eventually succeed in radioing the Alliance for help, only to learn that Colonel Stockton, the Warden of "the Anvil", has ordered the Alliance to nuke the area and kill everything that moves, supposedly to contain the infection and prevent the spread of the virus. Karina is soon captured by Alliance Security, and Mason finds himself fighting against the very organization he works for.

As Mason infiltrates "the Anvil" to retake Karina from Stockton, he finds the Scavengers have also launched a massive assault against the Anvil for revenge; Stockton masterminded the attack on Mason's transport, and that he has paid off the Scavengers to capture Karina for him but he turned out to have used them since he instead had The Alliance capture Karina for himself and refuses to pay them. Stockton is obsessed with battling the Shroud, and wants to use the virus Karina carries as a weapon against them. The Alliance had deemed Stockton's research dangerous, which led him to continue his project in secret.

Karina is a weapon created by the Shroud 30 years ago, but she was captured by the Alliance (specifically, Stockton's father) and cryogenically frozen. The virus she carries allows its host to generate massive amounts of energy from their bodies. This energy can be used to power Shroud weaponry and even to create a natural energy shield around the host's body. However, the virus and the energy it produces are also unstable, and hosts have a tendency to explode.

When Mason finally confronts Stockton, he learns that Stockton has infected himself with the virus, and gained the ability to produce an energy-shield, as well as the ability to operate a Shroud energy weapon, the "Titan's Fist". The Shroud soon attack to capture Karina, and Stockton proceeds to use his newfound powers to battle them.

Stockton attacks Mason to ensure that there is only one virus carrier, and Mason succeeds in killing him and retrieves Karina. Karina pleads with Mason to escape together with her far away from the conflict, but surprisingly Mason betrays her by turning her over to the Shroud. Mason is revealed as a traitor to the Alliance who has been collaborating with the Shroud from the start. His task was to retrieve Karina and deliver her to the Shroud. After turning Karina over, Mason questions the Shroud about his daughter, who had died some time prior to the game. The Shroud hint that they have the ability to bring the dead back to life but insist that Mason perform more "errands" for them before he will be allowed to see his daughter again. Mason then realizes that the Shroud will never honor their end of the bargain, and goes on a one-man rampage through the Shroud outpost using his viral powers and the "Titan's Fist". Mason defeats a few dozen Shroud soldiers, finally killing a mysterious viral-powered Shroud woman protected by several Shroud assassins. After finally reaching Karina, he finds her connected to medical equipment draining away her blood. Shroud soldiers close in on the area, and Karina tells Mason that he cannot rescue her, begging him to euthanize her. Mason cannot bring himself to kill Karina, and instead shoots himself. As Karina watches Mason die, her out-of-control emotions produce a massive energy wave that envelops Mason's body and obliterates the Shroud outpost killing everyone.