3. Alex Mercer - Prototype 2
It would be a mistake to label Mercer as a good guy since he was ultimately the one responsible for unleashing the virus that all but destroyed New York in the first place; plus he does eat random people to heal himself. He does struggle with his monstrous nature, though, and he ultimately stopped Manhattan from getting nuked, so he’s not all bad.
Somewhere between the first and second game he gave up on mankind, though, and unleashed another outbreak in New York. There’s no redemption for Alex this time around, and the new hero James Heller spends the whole game tracking him down to seek revenge for the death of his family. Heller grows to be just as powerful as Mercer and finally kills - and consumes - him in the final battle.
It’s doubtful anyone will feel too sorry for Mercer’ ultimate fate, with the whole attempting to wipe out humanity thing, but he did make for a compelling anti-hero throughout both games.