That makes you, the protagonist, the ultimate villain. Whatever the other bad guys you killed have done, your actions can never be justified.
I do not think so (I did not play it myself but know about the game)
He was a researcher , and the army wanted to put him down to eliminate the traces of the research. Breaking the vial with the virus to kill himself , and the bastards who tried to kill him was something most people intelligent enough (to realise they have no chance escaping alive) would do. The rest was simply his good luck, that he survived the infection.
The ultimate bad guys were of course those who commisioned to the company to invent such a virus.
Not entirely correct: What actually happened at Penn Station is that Alex got cornered by Blackwatch agents, panicked, and broke the vial. This was not him being suicidal, but it was him thinking "If I have to go, so does everyone else", which is entirely unforgivable. He was then shot by the Blackwatch agents, and died. The virus that he released consumed him and took the form of his body. He wasn't Alex Mercer anymore, he was the virus. I don't know if you can call it good luck how he 'survived' in virus form; he didn't seem all to happy about it himself.
There are two sides to this story, though: While Alex Mercer was the 'bottom line' responsible for the release of the virus, as without his actions there would be no outbreak, there is also a 'top line' responsible, as without their actions there would be no virus at all. Because there should always be
some justification for your actions in the game, at the end of the game you kill the top line person responsible: General Randall. It all began with testing the virus's predecessor in Hope, Idaho, and after that went horribly wrong, Randall decided to keep the two people who survived the Hope outbreak, Elizabeth Greene and her child, for research. "The mother and child are now military assets." Without that decision the virus would have been stopped entirely, and there would be no GENTEK or Elizabeth Greene.
But the saddest thing in this story is that everyone else's actions can be justified by some point of view. Director McMullen of GENTEK saw the unlimited potential of the virus: it could be used to "cure every ailment known to man". On the other hand, it could also incite it. That's why Blackwatch decided to pull the plug on the project; it was too dangerous. The sacrifice of a few lives are for the good of many, so they killed everyone involved. Unfortunately, that backfired on them, and Mercer released the virus in Manhattan. The Alex virus that became of this, started his killing spree for knowledge. He only wanted to find out who was responsible. Blackwatch and the USMC pulled out everything they had to stop him, and can you blame them? The Alex virus was a one-man army that would stop at nothing to get what he wanted. Of course they wanted him dead. Then the Alex virus released Elizabeth Greene, after which all hell breaks loose. Can you blame Greene? She's not acting consciously, "her brain was fried by the virus". But then, as the infection progresses, it becomes clear that this virus is different from the one in Hope, Idaho. It has a longer incubation period before actually zombiefying the infected, and it's much more contagious too. It becomes clear that the only way of completely stopping the virus is nuking the entire island of Manhattan. General Randall sets out to do just this. But the Alex virus interferes again, kills the general, and detonates the nuke at a safe distance. They say that, now that Greene and the Supreme Hunter are dead, the heart has been cut out of the infection, and the infected aren't as 'driven' and can be killed easily. But the researchers know that eventually everyone will get infected, and that there is no hope for saving Manhattan.
Wow, that was long. The whole game is really one big tragedy if you look closely. I'm wondering what happens in Prototype 2.