Prototype follows the story of Alex Mercer, an amnesia-stricken experiment. As the game begins Alex finds himself on the experimentation table with absolutely no memory of his past. The bewildered prototype emerges from an underground lab far below the heart of New York City, only to realize that there is a lot more going on in the outside world.
With no familiarity of where he came from or if he is even human, Alex is forced to slay to discover his past and take vengeance for what has been done to him. He soon discovers that he has the capability to devour the power of those whom he kills, taking their memories, skills, and even their appearance.
Above these newfound talents Alex is suddenly thrown into a war involving himself and two different powers. The Black Watch Special Forces, an unbearably mutated virus-infected population, and the prototype himself all wage war in the streets of New York City.
By interfering in fights between the game's factions, or even deliberately leading one force into another and triggering a fight, Alex can manipulate the speed and spread of the virus.
The whole game is revolved around a giant plot in which the developers explain is designed to echo real world government secrets.