he game begins with The Project sending three teams (Alpha, Beta, and Gamma) to gather technology that would help with reconstruction; the player assumes command of Team Alpha in Arizona. While gathering pre-war "artifacts", the Project fends off attacks from an organization called the New Paradigm, another major survivalist organisation, which is more advanced than the player's forces. Later however, it is discovered that a self-aware computer virus named 'Nexus' is actually controlling the New Paradigm.
After the player defeats the New Paradigm, they are assigned to Team Beta, which is based in Chicago and under attack by a faction called 'The Collective'. Again, the player starts out less advanced than 'The Collective' and it is discovered that Nexus is controlling this faction too. At the end of the campaign, Nexus launches nuclear missiles at Alpha and Beta bases, prompting the player to abandon the facility and move to the Gamma base.
Upon arriving at Gamma base, the player is immediately ambushed by the Gamma forces, which have already been taken over by Nexus. After the player survives the ambush and develops countermeasures to 'Nexus' infection, Nexus takes control of the remaining NASDA satellites and attempts to destroy the player. However, before he can succeed, the Project captures a NASDA missile site, and shoots down the orbiting laser weapons. It is learned that the scientist Dr. Reed, who was bankrupted by the US military, transformed himself into the Nexus virus and was responsible for the nuclear holocaust by infiltrating the 'NASDA' systems. At this point, the survivors of the Alpha and Beta bases arrive, and the three Project teams launch a full-scale assault on Nexus. The Project destroys Nexus and can begin rebuilding civilization.