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.