The capital appearance of Prototype 2 is Sergeant James Heller, a man who blames the deaths of his ancestors on Alex Mercer. Afterwards actual a suicide mission and getting adapted into the virus by Alex Mercer, Heller is searching to annihilate Mercer, who acts as the game's capital antagonist. Mercer's motives are unclear, but clashing the aboriginal he is not committed to endlessly the virus, but seems to be overextension it.
After the contest of the aboriginal game, Manhattan recovered from the antecedent beginning and anybody anticipation that the now called Mercer Virus was eradicated. 14 months afterwards Prototype, Manhattan has been abandoned again, due to a additional outbreak, one far worse than the aboriginal one, and blocked off from the added boroughs of New York City, which has been renamed New York Zero. The boroughs of New York accept been disconnected into three zones, the Red, Yellow, and Green Zone. Anniversary arena stands for how afflicted New York City is by the Blacklight virus. Most boroughs of New York Zero accept been infected.
The Red Area is Manhattan, home of Alex Mercer; in it the Blacklight virus grows unhindered. The Yellow Area is a triage breadth abounding of berth towns and the poor, it is actual awash and while the virus grows there, it is at a minimum and Blackwatch is application the Yellow Area as a petri dish. The Green Area is non-infected New York City, except there is a abundant Blackwatch presence. James Heller will accept missions in anniversary area and anniversary mission's adversity will depend on which area it takes abode in. Blackwatch is accustomed as application and authoritative NYZ, but they are said to apperceive that New York in fact belongs to Alex Mercer even admitting the closing is alone apparent rarely.