14 months have passed since New York Zero was infected and turned into a war zone. The responsible party is Alex Mercer, who has become a terror and his shadow looms over the city. In the new Prototype 2, you take on the role of Sgt. James Heller, a veteran soldier whose life was destroyed when Mercer released the deadly Blacklight virus, killing his wife and daughter. Now serving in the military, he tries to prevent the virus from escaping from New York Zero. Heller wishes to die and take as many infected with him as possible, but during the last military mission, his entire unit will be slaughtered by a group of infected, leaving him as the sole survivor. This will bring him face to face with Alex Mercer, the man responsible for the death of his family, his city, and his life. Filled with rage, Heller attacks Mercer, but his abilities are not the same as Mercer's. Mercer is impressed by Heller's ability to survive and now sees him as a valuable asset for his grand plan to infect him and turn Heller into his prototype.