Alcatraz kills it and manages to gather alien tissue from its corpse, which causes some sort of reaction within his Nanosuit. Alcatraz is unsuccessful, and the crash site is attacked by a Ceph soldier. Gould asks that he head for the crash site and search for any alien tissue samples. While on his way to Gould's laboratory, Alcatraz witnesses several CELL helicopters shooting down a Ceph dropship, which crashes not far from his position. Because of this, Alcatraz also faces combat with CELL operatives, who believe that he is Prophet because of his Nanosuit. Prior to the incident, Prophet had been targeted by CELL Commander Dominic Lockhart as an active biohazard due to having been infected with the Manhattan virus, and also in part due to ethical disagreements regarding the side effects of wearing the Nanosuits (with Prophet describing the wearers as 'Dead Men Walking'). Assuming that Alcatraz is Prophet, Gould gets in contact with him and asks him to take the Marines to his laboratory. He then kills himself so that the Nanosuit will stop associating itself with him and be able to assimilate with Alcatraz.

Left with no other choice since he himself has been infected by the Manhattan virus, Prophet gives Alcatraz his suit, the futuristic and high-tech Nanosuit 2.0. Delta Force officer Prophet saves Alcatraz, and is distressed with the situation, expecting the squad to support him. However, insertion goes awry, with the Cephaloids destroying the sub, and Force Recon Marine 'Alcatraz' being left as the only apparent survivor. Due to the breakdown in social order within New York City, Manhattan is placed under Martial Law, and under contract from the US Department of Defense, soldiers from C.E.L.L., a private military company run by the Crynet corporation, police the chaos.ДЄ United States Marine Corps Force Recon unit is deployed to New York City by submarine to extract former Crynet employee Doctor Nathan Gould, who may have vital information on combating the alien race. Set in 2023, three years after the events of the first Crysis, the game begins with news footage of a large outbreak of the Manhattan Virus, a gruesome disease that causes complete cellular breakdown, and panic about an alien invasion by the Ceph, the tentacled, squid-like alien race behind the incident of Crysis.

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