The protagonist of Prototype, Alex Mercer has been transformed by a virus into a shapeshifting weapon. He seeks to uncover the mysterious source of his abilities as well as fight the same virus as it consumes Manhattan.
History

Mercer and the Blackwatch
Alex Mercer originally works for Gentek, furthering the corporation's research into weaponizing the Blacklight virus. When he learns that the virus is derived from a human intentionally infected, he attempts to leak information to the outside world. General Randall, frustrated by the leaky security of the company's top secret work, orders the scientists to be executed. Alex Mercer receives word of his dangerous position and steals a vial of the Blacklight virus as insurance. Fleeing to Penn Station but cornered by security, Mercer threatens to shatter the vial, unleashing the virus upon the city. The guards do not back down, however, and open fire, killing Mercer but breaking the vial in the process.
Alex Mercer's body is transported to the Gentek morgue, but the scientists' do not realize that Alex has been infected by a weaponized form of the virus. The pathogen secretly consumes every cell in his body, replacing it with a viral replica. The process complete, Alex Mercer awakens to a baffled autopsy team. Soldiers open fire, but Alex realizes to his great surprise that bullets have little affect on him. With super strength, speed, and agility, he evades the military and seeks out his sister, Dana.
With the help of his sister and other allies, Alex Mercer fights to stop the virus from consuming the rest of Manhattan, battling the infected and the soldiers of Blackwatch.
Trivia