Developer: Radical Entertainment
Platforms: Xbox 360, PS3, Windows
Release date: Some time in 2012
New York City, stylized NYZ, has been divided into three regions. Each region stands for how affected New York City is by the Blacklight Virus, with the red zone standing for the most infected. James Heller will have missions in each zone and each mission's difficulty will depend on which zone it takes place in.
As stated by Radical Entertainment, Prototype 2 uses a new protagonist, Sergeant James Heller, and takes place 14 months after the original. James had returned to the tattered New York City from the war in Afghanistan to find that his wife and daughter were dead due to Alex Mercer accidentally releasing the virus when questioning Elizabeth Greene. This damages Heller emotionally, who then goes out on military's most dangerous missions, succeeding each time out of his rage, despite hoping to die. Unknown by Heller, he is being watched by Alex Mercer who has taken an interest in him. Alex Mercer is now the ruler of New York City despite having become a ghost, only being seen on rare occasions. During one mission, Heller succeeds in completing the mission but is mortally wounded and appears to be getting everything he wanted, but Alex Mercer shows up. Alex then infects him with the Blacklight Virus, turning Heller into a creature like Alex. For unknown reasons, Alex is now spreading the virus despite previously trying to stop it. Heller then goes on to tap into the Blacknet System to decide where to try and strike Alex, as he believes Alex to be behind the mutants (though it was actually Elizabeth Greene). As stated by Radical, the Heller vs. Mercer revenge story is the game's A-Plot and there is to be a more complex and multithreaded B-Plot.