Prototype is an open world game, much like Assassin's Creed and Grand Theft Auto but with a "little" twist. You play Alex Mercer, a shape shifter who is shrouded in mystery, the only thing you know is someone made you into a monster, and it's your job to find out who. You can blend with the populace or show them your true form and kill everything you see. There are many ways to accomplish your missions in Prototype. You can be aggressive and kill anyone or anything that poses a threat to you. You can also subdue your targets by disguising yourself as the enemy to close in for the kill without alerting more enemies to your presence. Whichever game play you choose, let me assure you that it won't be boring.

Prototype also set up a number of mini-events/missions where you can earn evolution points which you can use to upgrade Alex's abilities. Each upgrade can help you with future missions, so don't ever pass up on upgrades. Some skill upgrades are vital to progress through the game, and some can be extremely helpful in certain situations. Prototype has a wide array of combos and skills, but some are better than the others, so button smashing is NOT an effective way to execute some combos.

The most known ability of Alex aside from his shape shifting capabilities is that he is able to transform his limbs into different weapons. Just like his skills, these "Active Powers" has to be used in a certain situations to fully maximize Alex's potential. Aside from weaponry, he can also transform his left arm into a shield to deflect bullets or even cover his whole body with armor. These transformations doesn't mean Alex is immortal, it's the other way around, each transformation has some restrictions so sticking with one combo or transformation actually makes the game harder for the player. How you combo your moves and your powers will determine the outcome in every battle you come across.

Aside from the main story that the player follows in the main missions in Prototype, they can also hunt for "Web of Intrigue" targets that possesses miscellaneous information based on the main plot. These "Web of Intrigue" targets are scattered all over the map, although their information is not vital in completing the game itself, they do contain some tidbits that will make players want to learn more on what really happened to Alex Mercer.