: Alex confronts Elizabeth Greene , the original host of a similar virus from a 1969 experiment in Hope, Idaho. He eventually defeats and consumes her, learning that the military plans to nuke Manhattan to stop the infection.

: Alex infiltrates the USS Ronald Reagan with the help of a mysterious contact, who is revealed to be a Supreme Hunter —a monster that had consumed and replaced a Blackwatch officer named Captain Cross. The Ending

: Alex eventually learns he was a Gentek researcher who stole a vial of the virus as "insurance". When cornered by Blackwatch at Penn Station, he smashed the vial, releasing the virus and dying in the process.

Alex defeats the Supreme Hunter and flies the nuclear device into the Atlantic Ocean. Though caught in the blast, a small piece of his biomass survives and regenerates after consuming a crow. He remains in the city, reflecting that while he is "something less than human," he is also "something more". Prototype Wiki | Fandom

: Victims of the Blacklight virus who have mutated into violent monsters. Major Story Beats

As Alex hunts for the truth behind his existence, he navigates a Manhattan overrun by a viral outbreak and two primary factions:

In the original , the story follows Alex Mercer , who wakes up on an autopsy table in a Gentek facility with no memory of his past. He soon discovers he has gained terrifying shapeshifting abilities, including superhuman strength and the power to "consume" others to absorb their memories and physical forms. The Core Conflict