The game follows Alexander J. Mercer (voiced by Barry Pepper) who wakes up in a morgue in the basement of Gentek, a genetic engineering company based in Manhattan, sending a pair of scientists that were just about to perform an autopsy running. Alex escapes, and witnesses the scientists being gunned down by military operatives. Alex is discovered and attacked. He survives bullets being fired into his chest, and leaps over a wall to safety. He soon discovers he now possesses powerful shapeshifting abilities, superhuman strength, speed, agility, durability, senses, endurance, weaponry and the ability to "consume" people to gain their memories, skills and appearance. With no memory of his previous life, Alex decides to find and consume those related to the conspiracy in order to uncover the truth. During his quest, Alex faces two factions: the United States Marine Corps and Blackwatch, a Fort Detrick special forces unit dedicated to combating biological warfare; and the Infected, monsters created by a virus known as BLACKLIGHT that is overrunning Manhattan. Captain Robert Cross (voiced by Jeffrey Pierce), a Blackwatch officer, is given orders to find and contain Alex.

Alex makes contact with his sister, Dana (voiced by Lake Bell), who assists him in tracking down targets, leading to the infiltration of Gentek headquarters. He finds a young woman called Elizabeth Greene contained in the building. Greene is a host for BLACKLIGHT and upon her escape unleashes it upon Manhattan. Dana directs Alex to Karen Parker, his ex-girlfriend. She agrees to aid him in stopping the virus, while requiring Alex to bring back samples of the virus. Karen later leads Alex into a trap, where he is confronted by Cross. During their battle, Alex almost defeated Cross when Cross mentioned 'Penn Station', triggering a flashback that leaves Alex dazed. Alex is injected with a parasite that threatens to kill him. Alex seeks help from Dr. Ragland, a pathologist linked to Gentek. Ragland helps Alex remove the parasite and turn it into a weapon against Greene. However, it has no effect on Greene as her body rejected the parasite immediately, and the rejected biomass forms a monstrous being, the Supreme Hunter, which Alex kills.

The origins of the virus and Elizabeth Greene are uncovered through a contact: in 1969 the government tested the virus' predecessor in Hope, Idaho, designed to target predetermined races. The virus mutated into something far more deadly, and the whole population was infected. Elizabeth Greene was the sole survivor; an anomaly in her body's biology accepted the virus, rewriting her genetic code along with that of her unborn son, codenamed PARIAH. The remaining population of Hope, Idaho, was liquidated by Blackwatch. Greene and PARIAH were kept in captivity for further research.

Alex discovers his own past: Blackwatch shut down the Gentek project due to leaks and ordered all project personnel eliminated. Alex Mercer took a sample of BLACKLIGHT as "insurance". Eventually pinned down by Blackwatch in Penn Station. Alex, in a final act of desperation and vengeance shatters the vial containing the BLACKLIGHT, releasing the virus before being gunned down. The virus entered Mercer's bloodstream through the bullet holes and repaired his body at the cellular level.

The contact and Alex pump a new "BLOODTOX" biological agent underground in order to drive the virus above ground where it can be fought directly, causing Greene to emerge, encased in a towering monstrosity. Greene falls from the monster in human form once she is defeated, and is consumed by Alex. Through her memories, it becomes apparent that General Randall, head of Blackwatch, is prepared to destroy Manhattan with a nuclear weapon. The contact, revealed to be Cross. Alex with the Captains help, infiltrates the USS Ronald Reagan to stop Randall. Once Alex consumes Randall, Cross is revealed to be the Supreme Hunter, who assumed Cross' identity after consuming him, and attacks Alex, asserting that when Blackwatch leaves NYZ they will no longer be searching for infected, and that after he consumes Alex, he will then be strong enough survive the nuclear detonation. Alex defeats the Supreme Hunter and moves the weapon out into the Atlantic Ocean with a helicopter, where it detonates and catches him in the blast. His remains float back to the city and regenerate after consuming a crow.

During the credits, it is revealed that the public considers the military to have been the one who stopped the infection; a US Senator is heard telling the media that the events in Manhattan were a case of nuclear and biological terrorism, and promises retribution upon those responsible. Alex, reflecting on the events that occurred and the truth he uncovered about himself, claims he has "become something less than human, but also something more". After the credits, Manhattan is shown to be slowly recovering, the virus has been almost completely eradicated. Alex, standing on top of the Reuters Building in Times Square, comments that his work is almost done.