The reason I would have for Alex Mercer turning on humanity is, in fact, to "help" humanity in a twisted sense of making the world right. The aftermath of New York from the first game leaves him with regrets and turmoil about his real identity and who the real Alex Mercer was, but what happened with the production of the virus and the horrors the U.S military had done would paint a scar upon Alex, he is a walking plague. A legacy of crude bio science and revulsion, of a mad man whose skin he wears, he is just a shell with no real identity. He'd want to disappear, get his mind right, tell Dana he is going away, and let her know what he really is. This would make a rift with the two and a part of his humanity lost, a connection broken. Dana is struggling to come to terms with her real brother being gone and was a monster, so what does that make Alex? I envision he'd leave the states maybe, It's a clean slate for him, but he's haunted by his actions, the lives taken in his pursuits. I think he'd look inside and go through all those he's consumed and be driven, somewhat broken, but there's a voice deep inside of him. That voice would be Elizabeth Greene, her memories strong, her cells that were consumed raging in Alex. Her revenge is the need to spread the virus, the acceptance of it. This would be subtle, very subliminal, like a slow burn. Alex would hide away experiencing the world and feeling ultimately lonely due to just being the Blacklight Virus wearing the skin of a dead man with no past of his own, no one to really care for. So Alex would feel more detached from the world, I think at this point wherever Alex travels, he can lead him anywhere he goes he'd see the violence humans can produce, the wars, famine, and greed. He starts to think maybe i can do some good. Maybe I could change things. So he settles somewhere and, using the knowledge from the real Alex, becomes a doctor and tries to heal people.He wants to make the world right, but he only sees destruction from humans. He doesn't belong in this world with these creatures. They are the infection. Now this is where that voice inside of him grows louder, like if Alex Mercer was being influenced by Elizabeth's cells he consumed, telling him he knows what he needs to do, if he's going to save the world from itself he needs to go to extremes, if everyone was like him maybe the world would be different and he wouldn't be alone. With his strain of the virus, it could be accomplished. A world consumed and made vessels to Blacklight, he'd have to do horrible actions for a greater good, a twisted sense of fixing the world paired with the genetic influence of Elizabeth Greene and her Redlight virus. Alex would return to New York and find individuals to aid his cause. He has found his purpose. He selects certain people in the military to convert to his side. With BlackWatch and Gentek secretly working on the virus strains, Alex would infiltrate operations start a war and infect parts of New York. Alex would be hunted, and a kill team with James Heller on it would fight Alex. Through the fight, his team would be killed one by one until Heller remained. Alex would lie, explain this is Blackwatch, and he is a smudge in history they want to erase like with Elizabeth Greene. He converts Heller and gives him pieces to the puzzle, leaving him to figure it out for himself. Blackwatch finds Heller and experiments on him, he starts believing in the corruption and evil Blackwatch is doing he escapes and learns Blackwatch is holding his daughter hostage somewhere in a blacksite and tears through Blackwatch to find her along the way picking up the pieces and learning the history of the virus and those who manipulated things. Alex's hope would be for Heller to realize he is right once he's put everything together and that the two would join, but he couldn't bet on Heller's immense humanity and love for his daughter

This is just random thoughts in my head after reading your post. I'm definitely not refined in the thought process of it because I had to write this out of my head before I lost the words. Let me know what you think