The animated adaptation of Prototype is a direct sequel to the first game and a prequel to the second game. It centers around Alex Mercer continuing the search for his dark past.
Returning as the protagonist of the anime, Alex seeks to find out what kind of his person he was before he unleashed the virus on Manhattan. Aside from Blackwatch and the remaining Infected, Alex encounters new enemies along the path to discover the original Mercer's past.
A reporter from Japan with long black hair. She is Alex's main love interest. While appearing to be a reasonalable and hard working women, it is later revealed that her personality is similar to the original Alex Mercer, being manipulative, anti-social, irrational and extremely psychotic in Every way. Unlike the original Mercer however, Hana wishes to use the virus's power to her ends. She was revealed to be the real mastermind behind the second outbreak, as when Mercer angrily consumed the virus powered Hana, she possessed his body and took over his mind.
Alex's sister also returning from the game. Dana recovered from her wounds from the first game and went back to helping Alex.
Also returning. Ragland continues to help Alex solve his problem with the Blacklight virus.
After Peter Randall's death, General Nox took command of Blackwatch. Nox is a very mysterious and humorless man. He wears a glowing green lensed gas mask, a black trench coat, black cargo pants and a black leather suit.
The protagonist of Prototype 2 and the narrator of the story. After his fight with Alex, James seeks to understand what kind of person Alex Mercer was before the second outbreak.