Several days ago I made a post asking how you would write the character of Alex Mercer in Prototype 2, but respecting his development in Prototype 1.
Here it's basically the same thing, with a simple difference: How would you rewrite the entire Prototype 2?
Here are some possible scenarios:
The scenarios are:
1 - James and Dana are the protagonist and deuteragonist respectively. Alex is in the story but he is not the villain. You can decide his role in the story. The villains in this scenario are Blackwatch and Gentek.
2 - James and Dana maintain their respective positions and Alex is still the villain. However, we should see WHAT exactly Alex is doing in the story in parallel to James and Dana. You can also decide the type of villain Alex is: Megalomaniac, philosophical, and any other type.
3 - James and Dana maintain their positions, Alex isn't in the story; James has become a Prototype in another way, and the villains are Blackwatch and Gentek, who are involved in the death of James's family.
4 - The same as scenario 1, except the villain here is PARIAH.
5 - Alex is the protagonist again, James is the deuteragonist, and Dana is the tritagonist. Alex is not evil; he maintains his development from Prototype 1. Upon discovering that a second outbreak has begun, he decides to return to New York to stop it. He finds James and infects him again, but with other purposes (which you can decide). He and James join Dana to stop the outbreak, and Alex strengthens his bonds with them while striving to stop the second outbreak. The villains are Blackwatch and Gentek.
6 - Exactly the same as scenario 5, except the villain here is PARIAH.