Alex Mercer has a problem - or a gift - depending on how you view it. Thanks to a virus in his system, he has several deadly powers and can change his appearance into any person he consumes, which means the same thing as brutally killing the person he wants to be.
He was part of a genetic experiment at Gentek, but lost his memory about what happened. Now, he's looking for vengeance and his past. Elizabeth Green, on the other hand, infects more and more parts of Manhattan Island with a transmutation of the virus, converting people into mindless zombies or brutal monsters.
Prototype is an open-world game similar to Grand Theft Auto IV. The player controls Alex as he roams through Manhattan Island, taking in iconic scenery like Central Park and Times Square. He can sprint against a wall to climb and jump up to the roof fast, thanks to his supernatural jump ability and invulnerability to falling damage. Defending himself is easy with his powers - he can lift heavy objects, throw them at enemies, shape shift into any person he manages to grab and consume, and use claws, a shield, fists like boulders, or powerful lashes. He has to unlock these powers by investing evolution points gained from killing enemies and fulfilling objectives into upgrades.
These upgrades increase his sprint speed, give him new abilities, and enable new moves like gliding through the air. Some abilities can only be learned by consuming specific persons marked with a symbol over their head. The player also needs to replenish his health and uncover the Web of Intrigue, which fills in the blanks on Alex's background.
Mini-games and search for landmarks are other ways the player can earn evolution points. These mini-games range from kill/consume missions and waypoint races over the rooftops to fighting small skirmishes on either side of the military or the infected.
The more information the player collects, the more evolution points they gain. This is done by progressing through the storyline, getting gold medals in mini-games, and searching for landmarks and hints hidden around the island.