One of the best games I've played.
The story is cryptic and well told, and the idea with the Web of Intrigue gives a new way of telling the story. Plus it gives the feeling that you would like to find out more about the infection and where and who it comes from.
When taking a break from the missions, you can take on your own small personal conquests. The free roaming really gives a lot here. The battle between the Blackwatch/Military and the Infected is constantly raging all over the island and you can do yours, making sure that one base or Hive stops spewing out troops, tilting the balance a bit to the other side. Or you can take the small, but fun, side quests located across the island.
This gives the game an amazing depth and, if you're just a bit open minded, it may even give you a kick of satisfaction when you tear through a whole army with your bear hands ;)
The possibilities given to you are almost incalculable. Combos with claws, hammers, whips, armor, shield etc. gives you a chance to beat the s*** out of the poor enemies getting in your way in varied forms of punishment.
If you feel like playing a game that makes you feel like you could take on the world, and still win if you fight hard enough, then Prototype is the game for you.
Though the game has small flaws in the graphics, they aren't really that visible unless you are specifically looking for it. Still this doesn't lower the score I've given, because the game still provides so much fun and variety that, more than enough, makes this a game well worth playing.