In the second iteration of Prototype you play Heller, a man whose only purpose in living is to revenge his wife and daughter. He blames Alex Mercer for their deaths. Throughout the entire game, Heller must take down Blackwatch forces and mutants produced by the virus spread out by Mercer himself.
To achieve that, Heller must develop new mutant skills (longer tendrils, bigger hammers, longer jumps and so on). Heller can get consume everyone and through this can find out what Blackwatch intend to do.
The gameplay resembles the first Prototype game and brings nothing new.