Prototype

Characters

The game's protagonist is Alexander J. "Alex" Mercer (voiced by Barry Pepper), a shapeshifter suffering from amnesia, causing him to forget his previous life, including how he obtained his powers. As he attempts to uncover his past and stop an outbreak of a virus called Blacklight, which has overrun Manhattan, Alex comes into conflict with two factions: the United States Marine Corps and Blackwatch, a Fort Detrick special forces unit dedicated to combating biological warfare; and the Infected, people infected by the Blacklight virus, which turns them into violent monsters. The main antagonist is Robert Cross (Jeff Pierce), also known by his codename, "The Specialist", a Blackwatch officer tasked with containing Alex.

Supporting characters include Alex's sister Dana Mercer (Lake Bell); Dr. Bradley Ragland (Phil LaMarr), who helps Alex throughout the game; Alex's ex-girlfriend Karen Parker (Vanessa Marshall); Dr. Raymond McMullen (Paul Guilfoyle), founder and head researcher of bio-research company Gentek; General Peter Randall (Gordon Clapp), the head of Blackwatch; Randall's second-in-command, Ian Taggart (Richard McGonagle); and Elizabeth Greene (Kari Wahlgren), also known as "The Mother", a former test subject that hosts the Blacklight virus. Brian Bloom has a minor role as a Blackwatch commander whose appearance Alex assumes at one point. Additional characters are voiced by Dave Fennoy, Dave Wittenberg, David Andriole, David Lodge, and Diane Hsu.

Plot

Alex Mercer awakens with no memory of who he is in a morgue belonging to Gentek, a genetic engineering company in Manhattan, where he escapes and witnesses scientists being killed by military operatives. After surviving being shot, Alex leaps over a wall, soon discovering his superhuman abilities; including shapeshifting, superhuman strength, speed, and creating weapons from his body; as well "consuming" others to gain their memories, skills and appearance. Amnesiac, Alex seeks to find and consume those related to the conspiracy to uncover his past. This puts him against the US Military and Blackwatch, a black ops unit attempting to contain the Blacklight virus overrunning Manhattan.

Alex finds his sister, Dana, who assists him in tracking down targets, leading him to Gentek headquarters. There Alex encounters a young woman called Elizabeth Greene contained in the building, and a host for Blacklight. Upon her escape, Greene unleashes Blacklight upon Manhattan. Dana directs Alex to Karen Parker, his ex-girlfriend, who agrees to help stop the outbreak, having him find samples of the virus. However, Karen later leads Alex into a trap, where he is confronted by Blacklight commander Robert Cross. Alex nearly kills him, when Cross mentions 'Penn Station', triggering a flashback that leaves Alex dazed, before being injected with a parasite that threatens to kill him.

Seeking help, Alex finds Dr. Bradely Ragland, a Gentek connected pathologist who removes the parasite, turning it into a weapon against Greene. However, when Alex tries using it on her, Greene's body rejects the parasite, which transforms into a monstrous being: the Supreme Hunter. After seemingly killing the Supreme Hunter, Alex finds and kills Karen out of revenge.

Reaching a contact, Alex discovers the origins of Blacklight and Greene are revealed: in 1969 the government tested the virus' predecessor in Hope, Idaho, to target predetermined races. The town became infected, to no ill effect before Greene's infection. An anomaly in her biology accepted the virus, rewriting her genetic code, allowing her to control the infected. Hope's entire population was liquidated by Blackwatch, with only Greene and her son – codenamed "Pariah" – surviving. Both were kept in captivity for further research. With samples taken from Greene's blood, Gentek's team led by Alex synthesized the current Blacklight strain.

Through this, Alex's past is finally discovered; Blackwatch shut down the Gentek due to leaks, having all project personnel eliminated. Alex escaped and stole a sample of Blacklight as "insurance". When cornered by Blackwatch in Penn Station, Alex spitefully shattered the vial releasing Blacklight before being gunned down. The virus entered Alex's bloodstream through his wounds, repairing his body at the cellular level, granting his powers in the process. The contact and Alex pump a new "Bloodtox" biological agent underground, driving the virus above ground to be fought directly. Greene awakens encased in a towering monstrosity. Separating the two, Alex consumes Greene and learns that General Randall, head of Blackwatch, is prepared to destroy Manhattan with a nuclear weapon.

Alex, with the help of the contact – revealed to be Cross –, infiltrates the USS Ronald Reagan, where Alex consumes Randall. Cross turns on Alex, and is revealed to be the surviving Supreme Hunter, which consumed the real Cross and assumed his identity. The Supreme Hunter intends to consume Alex, becoming strong enough to survive the nuclear detonation and start anew. Alex defeats the Supreme Hunter, taking the weapon to the Atlantic Ocean using a helicopter, where it detonates. Seemingly destroyed, Alex’s remains float back to the city and regenerate after consuming a crow.

During the credits, the military are credited for stopping the infection, with the government considering the incident a case of nuclear and biological terrorism. A surviving Alex returns to the city until his work is over. Alex reflects on the truth of his past self; claiming that he has become something less human, but also more.