Prototype starts with main antihero, Alex Mercer in medias res. He is telling his story Metroid style and you have to relive the events that lead up to the twisted fate that awaits Manhattan Island. Alex's story starts when he wakes up on a morgue slab. He wants to know what happened to him and once he finds out he has been injected with a (pretty awesome) virus to become the ultimate killing machine
AND said virus is infecting the cities population turning them into mindless zombies, he is a little miffed and wants vengeance.
Vengeance is easily served with Alex as he runs around the entire island searching for clues to his next victim. (Victim is a loose term since most of New York is a victim to Alex's murderous rampages.) He travels through the city in the best of ways, like a friggin' superhero! Alex can run along the sides of building, he can dash while in mid-air, and best of all, he must have a bit of squirrel DNA because he can glide great distances with the aid of a viral membrane. Alex's movements grow with his virus, but although he can parkour his way over the Empire State Building, he stills needs to be able to defend himself.
Prototype isn't short on the offensive super powers. Alex has numerous powers at his disposal including a giant arm blade, enormous claws, and two ton hammerfists. Each of his abilities can be upgraded through the skill tree with EP, or "evolution points."
There are enough skills in this game to make Alex the most overpowered protagonist of all time. Seriously, there are over 100 different skills and powers to upgrade and just when you think the latest one you've unlocked is the coolest thing you ever saw, the next power blows it out of the water. That is the best thing about Prototype, the constant supply of improvements makes for an incredibly addictive experience that makes you want to keep fighting to earn the next power. It never feels like a grind.
If 100 different powers weren't enough to keep you awake for a few days, outside of the thirty main story missions, Prototype has events scattered all over the island just begging to divert your attention for a few hours. One event has you running through checkpoints for the best time, while another has you killing as many people as you can with an equipped power in a set amount of time. My favorite has to be the Web of Intrigue missions. Alex can absorb anyone he sees to give himself a health boost or just acquire their skills and memories, and Web of Intrigue focuses on just that. Dozens of people wander Manhattan with a marker over their head and that means Alex must absorb. Once absorbed, a short movie plays and it fills in the missing pieces of the backstory to explain Alex's murky tale a bit better.
With an open world game like Prototype, certain conventions usually come with the character. Most of the time, forcing a difficult decision or a moral dilemma on the main character plays a huge part of the narrative. Prototype curbstomps that idea and then blows it up with a thermal nuke. Alex Mercer is completely amoral. His hunt for who did this to him has made him lose all sense of humanity and there is no redemption in sight, just revenge. His loss is our gain because you can completely lose yourself too with such amazing super powers and when you are throwing a bus at a helicopter after elbow dropping a tank from a few stories up, who cares if a few civilians are caught in the fray?