Will there be a Prototype 2
Continuing from my lengthy spout of boredom over Prototype below the statements beneath this statement:
Yes.
At the 2010 VGA's, Prototype 2 HAS been announced. There is not much detail revealed, except that you play as Sgt. James Heller (Possible incorrect spelling), and you have to essentially "kill your maker", suggesting that Alex made you a mutant, and that you want to kill him.
There was a mix up with the storyline of Prototype amongst some people who didn't quite catch the movement of things, but the general drift is as follows.
You play as Alex Mercer, a recently dehumanized human being turned walking genetically-altered viral strain. You are responsible in many parts for the current unfavorable situation in New York City, and though you may not be guilty of wanton cruelty as you try to right the wrongs you committed, you have no qualms against mimicking a zombie horror flick as you eat brains, bodies, and other mutated humans and beasts to link together what the hell is going on around you.
That being said, Pariah does not show in the game outside of the Web of Intrigue.
Moving on from that simple fact...
The mutant you face at the end is the creation of Dr. Bradley Ragland's personal brew being injected into Elizabeth Greene, subsequently being puked out as a super hunter mutant, defeated once by you, rising like a bloody anthropomorphic ogre once again after you leave, trouncing the neighborhood behind your back, consumes the captain you love to hate, which is in time with the viral-vision glowing image of him shown in a cut-scene, and pops up again after you thought you had just finished saving the world to try and consume you too. Needless to say, you kick him in the face... and kill him.
... For those who still want to say Pariah was/is/became/spawned/raped/killed/etc Captain Cross or is Mercer:
(1) Pariah does not show signs of being infected, neither physically or genetically. The Super Hunter obviously does, and he showed under Infected Vision... which means he's infected while again Pariah is not. Keep in mind all these creatures are hosts and such for different variants of viruses. Pariah is a single entity, he is Pariah only, he is the natural release of the non-coding regions of DNA that fuel the viruses in the story, he is not a carrier of any virus. The reason he has so much in common with Alex Mercer is because Mercer himself is not a carrier as the virus overwhelmed his body and copied him. So Mercer is not so much a virus, but a higher being spawned from the altered virus.
(2) When Elizabeth Greene said "I am your mother," she was speaking to the hunters who popped up right after she left and you can hear respond even with "you are our mother" if you listen closely. So Mercer is not Pariah. When Dana said Alex was the only other one held captive there, she was right since they brought Alex back to Gentek dead as you see at the beginning of the game when he first wakes up as the virus.
(3) When you fight the Supreme Hunter at the end of the game... need I say more? He's a hunter, not Pariah, who became Supreme rather than Superior after consuming Cross and God knows who else after you defeated him the first time since Mommy was no longer around to keep him in check.
(4) Other stuff... I ran out of boredom... Figure the rest out yourself, it's an awesome game.