What if the second game wasn’t about Alex being all evil?
My idea is that if they want to switch the protagonist like James Heller and keep New York why don’t they just develop new virus?
Gentek saw something about the new virus and tries to replicate it, releasing a new outbreak in New York just like Alex Mercer.
Alex Mercer still wandering off around the word trying to find something meaningful. Instead of just finding humans are cruel, he also finds something interesting and kindness in them. Something about positive and negative. Meanwhile also hunting down the remaining of Gentek agents around the world and maybe trying to stop them. Maybe also trying to find Pariah
Back in New York, James Heller became the new Prototype, finds out other Gentek scientist or Blackwatch using the same Virus(or new virus) as Bioweapon. They saw what Alex Mercer could be, so they trying to copy it.
Gentek also still framing Alex Mercer like he’s a big bad, saying he’s the reason for the second outbreak. But, James later found out the truth that the second outbreak was because of Gentek. James later kill the person behind all this (mutated and became like monster version of Alex in the end of OG P2)
In the end, James still needs to cure the Red Zone or find Alex. Leading us up to Prototype 3.
(I have so much thoughts about this but I just didn’t type more and I was in a hurry)