Alex Mercer is a deadly superhuman with powerful abilities, and the main character and anti-hero of Prototype. Before he gained his super-human abilities, he was a scientist working at GENTEK. He stole a small sample of the Blacklight Virus so that he would have insurance for going missing. After he was cornered by the military at Penn Station, he broke the canister containing the virus, and was subsequently gunned down by the military. The virus infected him first, and then awakened taking control of Mercer. Mercer awoke to an autopsy, and killed everyone there, finding out he had the ability to absorb them into his genetic code, taking their memories, skills, and appearances.

With no memories, Alex is forced to track down, kill, and consume those who were linked to it, facing off in a crossfire between the Infection and Blackwatch special forces. He eventually contacts his sister Dana and girlfriend Karen Parker. Dana identifies targets while Karen promises Mercer a cure. It turns out that Karen was an imposter and makes a parasite supressing Alex's powers. Eventually he gains them back.

As the conspiracy unfolds, with an unidentified contact's help, it appears that Blacklight was built as a virus that targeted a specific race, but evolved into something far more deadly, killing Hope, Idaho except for Elizabeth Greene, whose genetic code was re-written. Her son also survived, and was taken by Blackwatch and code-named PARIAH. The government co-operated with GENTEK with research. When employees of GENTEK with knowledge of Blacklight started to disappear, Mercer attempted to go underground to steal a sample as "life insurance". He was cornered and killed by Blackwatch at Penn Station, but he then released the virus on New York City. The virus infected Mercer first, and by the time he was in the morgue the virus had copied him fully.

The contact tells Mercer to unleash another virus to drive the infection to the surface where Blackwatch can fight it directly. Elizabeth Greene, now a genetic monster, comes to the surface and Mercer kills her. He attempts to absorb the CEO of GENTEK but he kills himself before Mercer gets the chance. The government then prepares to nuke Manhattan, and Mercer is directed to consume Colonel Taggart to gain access onto the USS Ronald Reagan where the bomb is. The contact, Captain Cross, betrays Mercer and is revealed to be the Supreme Hunter, a powerful Infected. It battles Mercer on the deck but is killed. Mercer then detonates the bomb in the Atlantic, killing himself, but a pool of infected biomass regenerates him. Mercer muses the effects of his actions, and eventually, Manhattan is healing and Mercer stands atop the Empire State Building before jumping off.

At present, he is currently residing in New York City. It is unknown what he is doing at the time.