Alex Mercer has woken up in the morgue of a genetic engineering company, only to find that he has gained incredible superhuman abilities - from amazing agility to rock-hard strength that allows him to stop bullets fired at him. With the ability to 'consume' people and absorb their very beings, Alex sets out on a quest to discover what caused this mutation and who he is.

In Prototype, players are let loose on New York city, free to use deadly superhuman abilities in a fully open-world sandbox environment. Making use of his newfound abilities, Alex must fight the monsters created by a deadly virus, as well as the military trying to end his existence, all to discover the conspiracy behind his condition.