Prototype is a side-scrolling shooter. Controlling a cutting-edge prototype craft, you must save the world from an alien attack.
The ship has 4 different, always available, weapon systems. This makes the game a little bit more tactical than other shooters. Some enemies leave energy pills. These pills are necessary to upgrade your weapon systems four times.
The game has 5 different (and long) levels, including mountain and forest settings plus another planet.
In Prototype there are no extra lives. You have only one life, but you can always save your game.