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The plot of Prototype centers on a large conspiracy regarding an unnamed mutagenic virus currently infecting New York City. The effects of the virus have been witnessed before in the town of Hope, Idaho in 1971. After being released in Penn Station in New York, the virus spreads through the city, necessitating at first subtle government actions to combat it, then martial law and evacuation. Alex wakes up with heavy amnesia in a morgue under the scalpels of two HAZMAT-suited scientists and escapes dazed into the city. He then begins to come to terms with his powers (including the ability to absorb memories - which is crucial to piecing together his own), and makes contact with his sister, Dana Mercer. Dana assists him in finding members of the conspiracy, which include government officials, military personnel and employees of bio-engineering firm GENTEK, where it is revealed Alex was previously employed.

Alex encounters several characters, not all of which have currently been revealed. His primary physical antagonist is the Specialist, leader of the Blackwatch special forces branch of the US military. Other characters include Karen Parker, a researcher at GENTEK and Alex's former girlfriend, Pat McMullen, head of GENTEK, and Dr Ragland, a pathologist that assists Alex and studies the infected.

As Alex adds more and more nodes to the Web of Intrigue (by consuming people's minds), the virus begins to spread further and further through New York, and the military is forced to step up operations in order to prevent spreading further. The city is evacuated, quarantined and placed under martial law as the military moves in with a full-scale lockdown with tanks, infantry and air support. The virus grows stronger and stronger, mutating citizens of New York into various monstrous forms. As the conflict begins to consume the city Alex's actions will play a part in deciding the course of the battle and perhaps the ultimate victor. As the game features non-linear sandbox play, the player is free to explore the city with Alex's superhuman agility through the course of the game. Steve Mele, Art Production Manager of Radical Entertainment, said in a blog "Speaking of exploring, I know there is a severed human leg on a rooftop somewhere in the city which initiates a side-story when found."

The virus spreading through New York mutates its hosts into a variety of hideous, powerful creatures, which share a reddish-black color scheme similar to Alex's powers. There seem to be multiple variants of the virus; what affects the different strains have is unknown. Low-level infections cause zombie-like symptoms, causing horrible skeletal, muscular and skin deformities in victims, regressing them mentally to savage beasts. These infected become widespread across the city and extremely numerous but are easily killed by both Alex and the military. Larger, more powerful forms of the virus include the Hunter creatures, which are massive (more than twelve feet tall and appearing to weigh around a ton), extremely strong and very durable (capable of withstanding a tank shell and several strikes from Alex's blade attack before dying). Early video previews of the game showed Hunters with spikes, long claws, elongated heads and tails this variety called the "Hunter Brawler", but more recent videos depict them as huge mutated humanoids with reddish, hairless skin, bulging muscles and apparently empty eye sockets. A larger, more powerful and physically twisted Hunter called the "Leader Hunter" abducts Dana during the course of the game, necessitating a superpowered chase through the city by Alex with the military tailing.

The larger infected monster seen in video previews are Hydras, huge subterranean creatures that resemble a giant muscular tentacles erupting from beneath the ground. The Hydras use teeth-like appendages to throw cars and other objects at enemies and retreat underground when damaged.

The largest mutated monstrosity is the mother which is seen only in a short period of time on the Brutal Boss trailer. Rumors say that Mother is the source of the infection; it contains at least fourteen different strains of the virus.