Imagine you are the most powerful superhero in the world. Anyone who would stand in your way would be stopped dead in his tracks. Your power would inspire fear and awe to the masses as you walk around the streets of metropolis. Now multiply that tenfold and you got some idea of how Prototype is going to play out.
You're Alex Mercer, and something has happened to you. You wake up in a morgue not knowing quite what happened, but suddenly you're able to jump, sprint, and hit with tremendous superhuman ability that just gets more powerful. It's lucky you've got these super powers, because you're taking on the whole Manhattan to find out who's responsible for this.
Like Spider-Man 2 and Incredible Hulk: Ultimate Destruction, you're a superhero let loose in a sandbox city. You can go anywhere you want, do anything you please, causing utter chaos in your wake. The main missions are fun, and surprisingly the story holds up rather well amidst the chaos. The side missions are a great distraction, helping you become stronger and more powerful.
It may not be the best game ever made, but it's certainly the most fun game I have ever played. Top marks.