Prototype follows the story of Alex Mercer, an amnesia stricken experiment. As the game opens Alex finds himself on the experimentation table with absolutely no recollection of his past. The confused prototype emerges from an underground lab deep within the heart of New York City, only to discover that there is much more going on in the outside world.
The entire game is revolved around a giant conspiracy in which the developers explain is designed to reflect real world government information secrets.
"This is reality plus one fantastic element," says executive producer Tim Bennison. "That fantastic element is your shape-shifting powers, and how they are somehow linked to this epidemic.