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Prototype is a 2009 comic book made by DC Wildstorm that was released along with the game. It is written by Justin Gray and Jimmy Palmiotti, and with art by Darick Robertson and Matt Jacobs. It reveals more about Hope, Idaho, Elizabeth Greene, and the viral outbreak. There are 6 issues of the comic.
In 1969, 1st Lieutenant Peter Randall is serving in the Vietnam War. It is during this conflict that Randall shows a strong commitment to his duty and insurance in containing the "communist plague". While leading a squad in infiltrating a North Vietnamese military outpost, Randall is unexpectedly met by General Stillwell who informs him that he is being reassigned. When a hesitant Randall asks what he should do with his men, Stillwell kills them and states to him that it was an order.
Subsequently, Randall participated in leading a Blackwatch unit in infiltrating Hope, Idaho and securing the "package" (the Redlight virus) before the town was obliterated. Upon arriving into a seemingly deserted Hope, Randall and his team met with resistance and nearly being overwhelmed by the Infected. Randall and his remaining team managed to locate the package in a bunker underneath the town.
In 2008, Detectives McKlusky and Ella Garcia are summoned to the scene of multiple homicides on Manhattan's West Side. They arrive at a homeless commune in an abandoned subway where they are told to don hazard suits, and discover that the entire commune were savagely slaughtered. They learned from a forensic scientist that the victims were killed by some kind of unrecognizable animal/creature, given the study of the severe wounds and a bloody footprint trail that is found on the wall.
After successfully obtaining the package, Randall and his remaining men fought through many of the Infected that were experimented by Blackwatch. Upon reaching the surface, they are confronted by another unit led by Sergeant Sam Hendrick, who informs them that the entire town is compromised and that they are to take a fortified position in a hospital and await for their extraction.
In the present, McKlusky and Garcia study on the given information provided by the FBI on Alex Mercer following his recent attack on a military strike team. They examine Mercer's connection to Gentek, which McKlusky has some foremost knowledge on the private company and their practice of manipulating human genes, and bringing his suspicions that Mercer was working on a genetic weapons program for Gentek. The detectives are later called to a supposed terror attack. When asking a police sergeant as to what occurred, he answered that according to the many eyewitnesses they were attacked by monsters. At this moment, Blackwatch begins its operation in containing Manhattan and placing the city under martial law. Now General Randall observe the operation as he reminiscent his ordeal in Hope in which he lost his left arm from his encounter with Elizabeth Greene.
McKlusky and Garcia are caught in the middle of Blackwatch's intervention. They then drive to Soho where they meet McKlusky's associate and conspiracy theorist, Maxwell Robbins. Robins had a history of conflict with Blackwatch in which McKlusky and his partner came to him for answers. Robins explains that Blackwatch's presence was in response to the information he had hacked into concerning something "biological and deadly" is loose in the city and advise the detectives to leave the city as soon as possible. He is then suddenly shot in the head by a sniper.
Following Robins' sudden death, McKlusky and Garcia leaves his apartment and are held at gunpoint by two Marines. The Marines had no intention on leaving the detectives alive, but are quickly subdued and interrogated by the detectives. One of the Marines stated that they were given the order to kill anyone in an area designated "infected" in consideration to the chaos unfolding in Manhattan. The detectives then leave the Marines with their weapons. McKlusky and Garcia are later called and dispatched to 125th Street where it is the site of an infected attack. They learned that the military has cordoned off Broadway. There, the detectives investigate an abandon building where the incident took place. Suddenly the roof breaks down and a hunter appears before them. With their pistols having no effect on the creature, Garcia and McKlusky flees into a room and jumps out a window.
Peter Randall recalls the life of Elizabeth Greene. Elizabeth was born in 1951 and moving to Hope, Idaho with her father in 1967, two years before the infection occurred in 1969. Remarkably and prior to her infection, Elizabeth showed no unusual physical characteristics, no disabilities, nor any history of illness. Coincidentally, as if of a matter of fate, Elizabeth was among a group of hippies that accidentally discovered and sneak into an unfinished bunker that would be the research site of the Redlight virus, before the teens were forced out by the bunker's personnel. Since during General Randall's operation in 1969, Elizabeth infected Randall after biting his left arm, forcing him to amputate it. At the insistence of Doctor Raymond McMullen, Elizabeth was relocated to Governor's Island for further study until her escape in the present day.
General Randall receives news on Robins' death, which he had executed, and learned about McKlusky and Garcia presence at Robins' apartment. He orders a search for the detectives and their termination.
McKlusky and Garcia lands on a taxi cab and continues to flee from the hunter. As they make a run across a street, the hunter is killed when a speeding firetruck rams into it. After the detectives observe the dead hunter, they return to their car as Garcia shares her concerns with her partner that everything that has happened is beyond them and voicing to leave the city. Once they reach their car, a military helicopter shines its spotlight on them and are order by the pilots to exit their vehicle and surrender.
Meanwhile, General Randall orders Captain Robert Cross and his men to capture "Zeus" (Alex Mercer) at all cost as he is the only chance of containing the infection without resorting to "extreme measures." Cross understood his commands, and assures General Randall that they will capture Mercer no matter "how big the landscape is."
In a flashback, a then lieutenant Robert Cross participated in Operation Ice Storm in 1998 in which he along with a small group of Blackwach recruits had to investigate an infected underground city in Antarctica known as Springfield - housing Russian defectors and prisoners of war, mostly consisting scientists, KGB agents and along with their families. Cross and his men were told that they were to quell a supposed uprising after contact was lost with Springfield until encountering the infected, in which Cross became the sole survivor. He managed to rigged Springfield to explode and taking the infected along with it, and escaped to the surface where he is met by Peter Randall, who revealed to him that the entire operation is a kind of initiation and that it was all a test for Cross to enter Blackwatch.
McKlusky and Garcia are demanded by the chopper to surrender or be killed. Alex Mercer suddenly intervenes and tells the detectives to leave as he attracts the chopper's attention. Alex lets the chopper chase him and enters into an office building. He quickly runs into a hallway and consumes a janitor. Disguised as the janitor, Alex avoids the Blackwatch soldiers who were sent to find him.
Meanwhile, McKlusky finally decides to leave Manhattan. However, he knows only one way is through Grand Central, which is controlled by the military. But fortunately he knows that not every subway station is controlled by them, and hopes that he and Garcia can move underground to Grand Central and that they need disguises. McKlusky then sees three Marines looting a store and runs over them, killing them. Garcia is shocked, but McKlusky angrily points out that everything is turning into chaos and he only wants not only himself but Garcia to escape this alive. This brought a brief moment in which the two passionately kiss. The two then loot the Marines' uniforms and are soon confronted by Blackwatch soldiers. McKlusky quickly guns them down with an procured assault rifle, providing time for Garcia to escape inside the looted store. The two head into the store's back alley, where McKlusky guns down the remaining soldiers. McKlusky and Garcia then loots the Blackwatch's uniforms and weapons. They then enter a vacant subway station. McKlusky confesses his attraction to Garcia, which she also reveals her too. But shortly thereafter, they are discovered by a pack of hunters.
McKlusky and Garcia runs for their lives from a pack hunters. Garcia stops running and decides to shoot them, causing one of the hunters to step on to the third rail, electrocuting it and its body explode. McKlusky and Garcia runs into a room, where a hidden hunter grabs McKlusky by the throat. Garcia attempts to shoot it, but shot McKlusky in the leg. The hunter throws both McKlusky and Garcia out. The hunter destroys Garcia's gun and pins her from reaching McKlusky's weapon. McKlusky attempts to strangle the hunter, but his left arm is bitten off. As it is distracted, Garcia grabs McKlusky's gun and kills the hunter.
McKlusky lapses into shock from his wound and is urgently brought out of it by Garcia. Weakly, McKlusky tells Garcia that he is infected and that he is changing. McKlusky also tells that he is hearing the voice of Elizabeth Greene, who is acting as the leading hive mind of the creatures, and learns that she is deeply afraid of Alex Mercer, which he believes Mercer is the one who could stop the infection. McKlusky tells Garcia to leave without him before he turns. He then commit suicide with a gunshot to the head. Unfortunately, McKlusky's body mutates into a monster. Garcia immediately guns down the mutant McKlusky before walking down the tunnel.
Above ground, Manhattan descends under martial law and the island is quarantined from the outside while the news media calls the infection as the "worst viral outbreak in American history". As this is happening, Garcia has succumbed to the Blacklight virus from kissing McKlusky before he had turned, transforming her into an infected. She emerges from the tunnel where Blackwatch soldiers spot her and attempt to gun her down. However, the soldiers are quickly slain by her and the infected Garcia makes her move to apparently outside of Manhattan.