The opening of the game starts with a Scientist mixing some chemicals, when his facility is attacked by an unknown hostile force. He avoids some of the enemy forces but gets cornered and has to fight off some enemies. He is then saved by a Commando from the Strike Force Squad. The Commando has a few questions for the Scientist, setting in motion the central storyline.
The plot jumps to a flashback that will lead up to the events in the Facility. The story takes place in modern times and starts with a Strike Force squad putting down a rebellion in South America. When leaving after the mission, their plane gets shot down. Unknown hostiles have boarded the plane, but the Strike Force takes them out regardless and at the end of the battle, parachute dramatically before the plane explodes.
The Player lands with part of the Strike Force, inculding the pilot and sniper named Jenkins, but something goes wrong. All of them were infected with some sort of virus and go berserk. The Player guns them down and investigates an explosion on a nearby research facility.
The Player saves a Scientist (the one from the beginning) in the facility and interrogates him. The scientist says the reason why Player's squad went berserk was because of a experimental nerve toxin to counter infantry. The toxin was intended to paralyze the soldiers mentally and make them lose there will to fight but instead of making a subject lose the will to fight, they went berserk with uncontrollable rage by shutting off all of their brain's activity except for the reptillian section. The scientist then tells the Player that he can make a cure from an enzyme of a very special plant.
The Strike Force then goes and extracts a cure from a plant in the area but is ambushed by the same unknown enemy. After interrogating one of the enemy soldiers, the Strike Force attacks their HQ set in a foundry, and steals some key intel.
The name of the enemy is Globex, and they are planning to attack the Research Facility to destroy the toxin. The Strike Force intercept them outside the Facility and force them to retreat. They then clean the Facility of the infected and allow the Scientist to finish his research. The Strike Force then head back to Globex HQ and find out their next plan. After a battle, they find out that Globex is going to launch a nuke to, in essence, destroy the country to prevent the toxin from spreading.
The Strike Force tries to stop the launch by intercepting the Nuke's transport. They are too late and the Nuke is launched. Then, cinematacally, Player is flown to the Nuke, jumps onto it and switches the nuclear payload for the Cure, allowing it to be deployed in the atmosphere.
Before the Player can leave, the leader of Globex confronts Player and they have a showdown. Player defeats him and leaves the nuke before it explodes with the cure in place, leaving the Globex Leader to die in the explosion.
Several weeks later, the Scientist is called by the leader of Globex, who actually survived the detonation of the nuke over the telephone. He states his regret over being unable to stop the Player, but his success in obtains samples of both the Toxin and Cure. The Scientist's motives are unknown.
- The story starts and ends with the Scientist in the cutscene.
- Both in this game and Raze, zombie-like viruses are involved.
- The story ends with a cliffhanger and the story is continued with the second game.
- The Player in the mission "under siege" is displayed as a Commando, tought when the story comes to the "siege under" mission, the player can choose freely among all classes.
- The detective achievement is the only secret not avaiable in quick match.