The player is cast as James Heller, a soldier whose family was killed in the viral mayhem unleashed upon Manhattan by former protagonist Alex Mercer while Heller was serving overseas. He returns to New York 14 months after the original outbreak as part of a clean-up effort, intending to die fighting the viral outbreak and be with his family. Instead, their paths cross and Mercer personally infects Heller with the Blacklight Virus. Thereafter, Heller dedicates himself to hunting and killing Mercer, no matter the cost.
Since the Manhattan outbreak of the Blacklight virus, New York (NY Zero, as it is now referred to) has been split into three different sections based on that area's level of affliction. The corporation responsible for the virus’s creation, Blackwatch, has covered up its malicious acts by placing blame on Mercer. His actions from the first game, typically based on saving the lives of innocents, are twisted to look like sinister acts.
Before Prototype 2's official announcement, a teaser website showed a five second clip that contained huge black tentacles, a big monster, and "I love NYZ", revealing that the game will be set in New York City once again. The clip closed with the words "Murder Your Maker."
The game was confirmed at the 2010 Video Game Awards.
James Heller is a former mildly-decorated soldier from the war in Iraq. Despite issues with post traumatic stress and an insatiable will to kill Alex Mercer (the person he blames for killing his wife and daughter), he is assigned to Blackwatch, a military organization, in the red zone of the infected New York City (now known as New York Zero). Heller and company were attacked by Mercer, and despite frequent attempts to slay the man, Heller fails in his revenge quest and is subsequently infected by the Mercer Virus by Mercer himself.
Heller next finds himself taken back by Blackwatch in order to be experimented upon. However, despite showing fighting skills, the testers are wary of another experiment gone wrong and decide to kill Heller. Heller escapes but is confronted by Mercer, who asserts that he didn't kill James' wife and daughter and that Gentek and Blackwatch are working together to conduct a biological weapon experiment within NYZ.
First, Heller goes to Father Guerra for spiritual guidance, but Guerra explains that no one messes with Blackwatch. Heller himself then goes out to not only decapitate some commanders, but also to stop Blackwatch from using their infected test subjects on the local population, convincing Guerra to work with him. Heller then proceeds to kill and consume the memories of more and more Blackwatch and Gentek personnel to understand and stop the nature of Gentek's plans. He is also trying to kill Colonel Rook, who ordered Heller's execution once infected with the Mercer Virus. Soon, Heller learns that Gentek has finished studying "Phase One."
Heller's main abilities are shapeshifting and absorption. He can consume other humans, taking in their physical appearance and memories. However, there are instances when Heller takes attributes from certain infected test subjects, such as claws and tentacles, adding to his offensive arsenal.
Prototype 2 is an open world sand box game built for easy navigation. James can easily run on walls, enabling him to climb buildings with little trouble. In the air, he can glide and mid-air dash in order to keep himself airbourne.
In battle, Heller can use dodge moves to evade opponents. Offensively, he can use his bare fists for either quick combos or heavy attacks. When his health bar is low, he can grab any human character and consume them, taking on their likeness, and absorbing bit of health. Each biological weapon has its own special attack (ie. "Pounce" for the claws and "Black Hole" for the tentacles). There are also weapons lying around, like guns and bazookas, that Heller can use to his advantage. James can also hijack military vehicles (ie. helicopters) for his own uses.
As there are many military officers around, Heller needs to keep a low profile. Once spotted, however, he will be fired upon until he can escape. To get the jackboots off his back Heller needs to break line of sight in order to completely empty a circular bar that represents the police's willingness to pursue him. Disguises are often Heller's best friend.
Every so often, James levels up and can improve important aspects of himself such as health and speed. There are further upgrades depending on Heller's actions (offensive, defensive etc).
There are hidden items to find in each sector of the world (like black boxes) that can further improve Heller's attributes and even provide backstory.
The soundtrack for Prototype 2 is composed by Scott Morgan and the list is :
Activision and Radical Entertainment released a collector's edition for the game titled "Prototype 2: Blackwatch Edition"
It's contents include: