Prototype is an action-packed video game set in Manhattan, where people are mutated into bloodthirsty monsters. The protagonist, Alex Mercer, wakes up in a morgue with no recollection of his past and discovers his superhuman abilities. He can absorb people, take their appearance, and gain their knowledge. Alex fights against the epidemic and hides from the army, police, and mercenaries who consider him guilty of creating and spreading the virus.

The game offers an open-world environment where the player can move vertically and horizontally on the walls. Alex can jump high, run on walls, and plan in the air. He uses his body's transformation ability to fight by turning his hands into sledgehammers, blades, whips, or shields. He can also use armor and see in the dark. The game has a wide range of weapons, including assault rifles, machine guns, grenade launchers, and rocket launchers. The player can improve their abilities as they progress through the game and complete various missions.