Part 3 Visiting Alex Mercer’s Apartment and getting to know who he is.
Alex Mercer wakes up in a morgue in the basement of Gentek, a genetic engineering company based in Manhattan, scaring away a pair of scientists that were about to perform an autopsy. 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 abilities, including shapeshifting, 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, quickly bringing him into conflict with the US Military and Blackwatch, a black ops unit trying to contain the Blacklight virus which is overrunning Manhattan.
Alex makes contact with his sister, Dana, who assists him in tracking down targets, leading to the infiltration of Gentek headquarters, where Alex encounters a young woman called Elizabeth Greene who is contained in the building. Greene is a host for Blacklight, and upon her escape, she unleashes it upon Manhattan. Dana directs Alex to Karen Parker, his ex-girlfriend, who agrees to aid him in stopping the Blacklight outbreak, asking him to bring her samples of the virus. However, Karen later leads Alex into a trap, where he is confronted by Blacklight commander Robert Cross. During their battle, Alex almost defeats Cross, until Cross mentions ‘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. Bradely Ragland, a pathologist linked to Gentek. Ragland helps Alex remove the parasite and turn it into a weapon against Greene. However, when Alex tries using it on her, Greene’s body rejects the parasite, which then transforms into a monstrous being: the Supreme Hunter. Alex defeats the Supreme Hunter, and later finds and kills Karen as revenge for setting him up.
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. Although the entire town was infected, no ill effects manifested until Greene’s infection. An anomaly in her body’s biology accepted the virus, rewriting her genetic code and causing her to take control of the infected town, becoming hostile in the process. The entire population of Hope, Idaho was liquidated by Blackwatch with only Greene and her son, codenamed “Pariah”, surviving. Although kept separate, the two were held in captivity for further research. With samples taken from Greene’s blood, Gentek’s team led by Alex synthesized the current strain of Blacklight virus.
Alex also discovers his own past: Blackwatch shut down the Gentek project due to leaks and ordered all project personnel eliminated. However, Alex disobeyed the order and took a sample of Blacklight as “insurance”. Eventually pinned down by Blackwatch in Penn Station, Alex, in a final act of desperation and vengeance, shattered the vial containing the Blacklight, releasing the virus before being gunned down. The virus entered Alex’s bloodstream through the bullet holes and repaired his body at the cellular level, giving him his powers in the process.
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. Alex, with the help of the contact – revealed to be Cross – 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 (New York Zero, the name given to the city after the outbreak) they will no longer be searching for infected, and that after he consumes Alex, he will be strong enough to 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.
source