Prototype

The game follows the story of Alex Mercer, an amnesiac who wakes up on a morgue slab in the basement of GENTEK, a large and influential genetic engineering company. After an encounter with several armed soldiers, Alex escapes and sets out to recover his memory and find out exactly what occurred. He soon discovers he now possesses powerful shapeshifting abilities that grant him tremendous strength, speed, weaponry and the ability to "consume" people to gain their memories, skills and appearance. With no memory of his previous life, Alex is forced to track down and consume those related to the conspiracy in order to uncover the truth.

During his quest, Alex faces two factions. One is the military, composed primarily of Marines fronting a ruthless black operations unit known only as Blackwatch. Blackwatch is a Fort Detrick special forces unit dedicated to combating biological warfare. Captain Cross, a Blackwatch officer, is specifically given orders to find and contain Alex. As Manhattan slowly begins to fall apart, Alex also faces the Infected, consisting of civilians who have contracted a strange virus and powerful monsters known as Hunters.

Alex then makes contact with his sister, Dana. Dana assists him in tracking down targets who can shed light on his past, leading to the eventual infiltration of GENTEK headquarters. Alex finds a woman called Elizabeth Greene contained on level 51 of the building, who escapes and takes control of the Infected. After continued work with Dana, Alex makes contact with his ex-girlfriend Karen Parker. Initially, Alex trusts her as he helps collect Infected genetic material for her research. However, it becomes apparent that she's with Blackwatch when she uses it to synthesize a suppressant for Alex's shapeshifting abilities, which Captain Cross later injects into Alex. With Dana's help Alex meets Dr. Ragland - a pathologist linked to the whole matter. After several missions, Ragland formulates a cure for Alex, as well a weapon to use against Greene herself.

When Alex next returns to Dana she is kidnapped by a massive "Leader Hunter" who escapes Alex due to military interference. He returns to Ragland for help, eventually discovering Dana's location. Within that hive, he finds and confronts Elizabeth Greene, injecting the weapon into her neck. She vomits out the resulting mix, which forms into the Supreme Hunter which Alex defeats. Alex then finds Dana unconscious and brings her back to Ragland's lab.

As the conspiracy unfolds and with the assistance of an unidentified contact, the origins of the virus and Elizabeth Greene are uncovered: in 1969 the government had tested the virus' predecessor in Hope, Idaho, designed to target predetermined races. The virus then mutated into something far more deadly, and the whole Hope population was infected. Elizabeth Greene was the sole survivor; an anomaly whose body accepted the virus, rewriting her genetic code along with that of her son, who was taken from her by Blackwatch. The remaining population of Hope, Idaho was then liquidated by Blackwatch soldiers in "Operation Altruistic". Greene and her son were kept in captivity for further research, later in conjunction with GENTEK.

Soon after Alex discovers his own past: Blackwatch shut down the GENTEK project due to leaks and ordered all project personnel eliminated. GENTEK employee Dr. Alex Mercer attempted to go underground and took a sample of the virus (Dx-1118 variant A) as "insurance". Eventually pinned down by Blackwatch in Penn Station, he decides to take down as many as he can with him, shattering the tube and releasing the virus ("BLACKLIGHT") onto the unsuspecting city. After he falls from being shot, the virus enters his corpse, consuming and copying Alex's entire body. Upon waking in the morgue at the start, the virus clone believed itself to be Mercer.

The contact and Alex assist the military in pumping the new "Bloodtox" biological agent underground in order to drive the hiding virus above ground where it can be fought directly. The plan works; Elizabeth Greene emerges as a towering monstrosity, whom Alex defeats and consumes. They then falsely attack the Bloodtox facility in an attempt to reach GENTEK's head researcher, Dr. Raymond McMullen, and obtain answers from him. Dr. McMullen tells Alex about his history with GENTEK, but when asked about Hope, Idaho he shoots himself in the head, ensuring that the secret is taken to the grave. It becomes apparent that Randall, head of Blackwatch, is prepared to destroy Manhattan with a nuclear device. The contact, revealed to be Cross, tells Alex to consume Blackwatch officer Colonel Taggart as a means of infiltrating the USS Ronald Reagan, where it is held. Once Alex consumes Randall, Cross reveals himself to be the Supreme Hunter - having survived their last fight and consumed the real Cross to assume his form. Mercer defeats it through decapitation, then begins to move the weapon.

He manages to fly it out and drop it in the Atlantic Ocean, where it detonates safely but catches him in the blast. His remains float back to the city, regenerating after consuming a crow and thereafter musing on what he has become: "I am something less than human, but also, something more.