It's fun to be an anti-hero. They get to be completely self-involved while causing untold billions of dollars in damage and thousands of deaths, leaving a trail of havoc and charred wreckage wherever they go. They may be total douchenozzles but they're a lot of fun to play.
Alex Mercer is another in a long line of sociopaths let loose in a city that's too fragile to contain his temper tantrums. He's been infected with a virus that's made him almost indestructible and given him the ability to shapeshift, and the military wants his head on a platter. The virus is also spreading through Manhattan and turning people into murderous shambling wrecks, but that's just collateral damage in Alex's quest to find out what really happened to him and make those responsible suffer.
So, no, you don't go to Prototype looking for story, despite its best efforts. Prototype is a straight-up action game set in the sandbox of Manhattan in which the whole point is to cause as much chaos as possible. Alex initially starts out as a total scrub, strong and durable but little more, but as the story missions go by and new powers get added on he becomes a nearly-unstoppable force of nature. A typical encounter might see him bludgeon a couple of tanks with the hammerfist, switch over to arm blades to whittle down the health of giant mutant brutes before grappling and consuming them for a large health boost, change powers again to the whip fist in order to grab and hijack a helicopter, and then, after clearing out the remains of the strike team sent against him, pump a ton of missiles into the mutant base to see it collapse into a pile of rubble. That's neither a story nor side mission, but rather just some random trouble run into while traveling the map.
Prototype does its best to keep things going chaotically mad, with ridiculous levels of destruction happening everywhere. There's no way to go wrong with that.
For action with a bit more purpose, Prototype focuses its gameplay on three types of events- story missions, side mission, and the usual collectible hunt. Collectibles come in two kinds of orbs and wandering people who posses a chunk of information that fills in holes in the backsotry. Landmark orbs are standard fare, scattered throughout the city waiting to be picked up, but hint orbs are a bit weirder. Picking up a hint orb gives some gameplay advice, but is it really necessary to be told about holding down the throw button to charge up the move for extra damage when 20 hours into the game?
While the collectible hunt wears out its welcome once the items start getting scarce, the side missions fare much better. Most of them are combat oriented, requiring Alex to take out a certain number of enemies using a specific weapon or power, or fighting on the side of the mutants or military against the opposing side. There are also races, which tend suck pretty badly thanks to a control scheme suited to locking on to enemies rather than fine manual adjustments, and glide events, in which Alex flies off a building and tries to land as close to a target as possible. The glide events in particular make for a great change of pace from the wanton carnage, and it's very easy to get caught up in shaving another foot or two off the top score. While the side missions have absolutely nothing to do with the main story, they tend to be fun enough that their tacked-on nature is easily ignorable. Besides, who needs a reason to take out as many mutants as possible in a given time using a grenade launcher, aside from all the lovely explosions and bloody carnage?
Random violence aside, the story missions that drive Alex's tale of revenge show a lot of variety in bringing a bloody beatdown to everything in his path. He'll need to use all his skills to not only bust heads but perform stealth kills to consume important personnel and temporarily assume their identities in order quietly access sensitive areas, or destroy poison-spewing gas jets before being overwhelmed by the toxins and heavy military firepower, or even perform escort mission that, in what must be a first in gaming history, aren't a complete chore. The story mission objectives are varied enough that the tasks never become repetitive, and the generous checkpoints mean you can experiment with tactics without fear. Death will happen a lot, especially during boss fights, but the penalty rarely feels unfair.
Despite a few missteps, Prototype is a lot of fun. Most of the time it focuses squarely on over the top action, with huge fights leaving the city streets strewn with body parts and smoking mechanical debris. Alex gains a good variety of powers (with special moves available for each), uses guns and armored vehicles to great effect, and has endless waves of enemies to practice his skills on. There are some odd gameplay decisions here and there, such as the horrible checkpoint races, and Alex is both unlikeable and not very interesting as a character, but with the sheer volume of asses to kick and the number of ways to kick them those problems are easily overlooked once the game gets properly underway. Prototype does its best to keep things going chaotically mad, with ridiculous levels of destruction happening everywhere. There's no way to go wrong with that.