Uh-oh, looks like the Prototype franchise will end for me sooner than expected. Well, judging from what data I have anyway, maybe I just don't know enough of the game to understand anything at all just now.
Don't get me wrong, making Mercer (and by "(Alex) Mercer" I mean the identity the virus has developed by the end of the game, not the original person) the antagonist is - in itself - nothing bad, it even has the benefit of letting you start from zero again with a new character and delivering a powerful enemy at the same time. I do prefer it to making bad excuses about new enemies and how the protagonist of the prior game gets depowered.
But I'm afraid Mercer is getting the Idiot Ball this time, and there's nothing more dissatisfying than defeating an idiot and being portrayed like it's a great achievement.
I could excuse Alex Mercer becoming the villain despite him saving the city, despite him defeating the Redlight Virus, despite him developing real emotions and attachments to humans. After all, he was betrayed numerous times and as a virus he probably could have some deep instinct of acquiring more biomass or enlarging his territory - that part could be excused somehow, even if it wouldn't satisfy me because it would mean degrading the entire character development for me - back again to animalistic instincts from a complex and troubled existence that is unsure about its own identity, purpose and fate.
In fact, in the end, he is filled with regret and self-despise in my opinion, he hates the part of him that started the infection, even tho it meant he got to live, this new existence came to be, at the price of the lives of others.
He, ultimately, puts the lives of others ahead of his own and goes to extremes to that. That makes him an unlikely hero, an anti-hero for me, someone who slaughters hundreds, thousands of peoples to reach his goal, which is, in the end, saving others. We got no canon info about how he handled civilians after all, so we can't even say he killed or nom'd innocents (on purpose) at all.
He could've just ditched New York and flown away in a helicopter after all (and even with the "animalistic" traits of a virus it would've made more sense to start anew somewhere less dangerous), but I guess it was his sense of responsibility that made him follow a different path without questioning it.
It might be over-analyzing, but seeing the amount of Fridge Brilliance everywhere in Prototype, I can't help but think the writers did put a lot of effort into developing this rather complex and intriguing character once you get behind his potato face.
And now he's powering up some random dude and makes him angry.
There's just no excuse for that. Not even if Alex was bored and wanted a toy to play with, he knows what it's like to be a toy, a lab rat, I don't think he'd be egoistic enough to do something like that after the first game's events. He knows how quickly this stuff can get out of control, he, as a researcher and the blacklight virus in itself, knows how unpredictable and versatile these superpowers can get.
It's always so boring to see villains that impose challenges onto themselves and then they ultimately get defeated by their own arrogance. It's just so cliché and such a common way to make the victory graspable for a new hero against a villain that knows all the tricks.
/rant