Crysis 2 is a first-person shooter . The player assumes the role of a Force Recon Marine called Alcatraz. Similar to its predecessor, it provides freedom to customize weaponry and abilities. Crytek wanted to avoid making another game set in a true jungle environment New York City has been dubbed an "urban jungle". The urban atmosphere offers new options with relation to progressing and planning attacks. Players are able to navigate between floors and buildings, as well as a destroyed cityscape.
A United Mariens Corps Recon unit is deployed into New York City by the submarine USS Nautilus to extract former Crynet employee Doctor Nathan Gould, who may have vital information on combating the alien race. However, insertion goes awry - the Ceph, the alien race that is trying to destroy humanity, sinks the sub, and Force Recon Marine "Alcatraz" is left as the only apparent survivor. Delta ForceMajor Laurence "Prophet" Barnes saves Alcatraz and is forced to kill himself in order for his Nanosuit to assimilate Alcatraz. A recording left in the suit reveals that Prophet had been infected by the Manhattan virus, and that Alcatraz is to finish Prophet's mission to rescue humanity from the alien invasion. Believing Alcatraz is Prophet, Gould soon gets in contact with him and asks him to meet up at his lab. However, CELL forces, led by Commander Dominic Lockhart, target Alcatraz and label him as a major bio-hazard, believing him to be the infected Prophet. This forces Alcatraz to combat CELL troops throughout Manhattan as he makes his way to Gould's lab. While on his way to Gould's laboratory, Alcatraz collects alien tissue samples from a crashed Ceph dropship and a Ceph soldier, which cause strange reactions within his Nanosuit, giving him some alien abilities. Alcatraz eventually meets with Gould, who is initially hostile after learning that he is not Prophet. However the last suit recording of Prophet's message causes Gould to relent, prompting Gould to explain that the suit has been busy rewriting its own code after absorbing the Ceph's tissue, speculating that the suit was creating an antibody for the Manhattan virus. Gould and Alcatraz commit to further scans at a Crynet base on Wall Street. They find out that Alcatraz was mortally wounded when Prophet rescued him, and that the Nanosuit is the only thing keeping Alcatraz alive. The scans are cut short when CELL forces led by Commander Lockhart and Lieutenant Tara Strickland, daughter of U.S. Marine Corps Major Strickland from the first game, ambush Alcatraz and Gould.
During the middle of a prisoner transfer outside of the building, the Ceph attack the CELL personnel as a massive alien spire rises from underneath the Crynet building, releasing a spore-based bioweapon that kills most of the CELL troops in the immediate area. Alcatraz is left stranded and isolated for a period of time while dealing with a Nanosuit malfunction caused by the spore bio-weapon. The suit gets rebooted remotely by Crynet director and Hargreave-Rasch Biotechnologies co-founder Jacob Hargreave, a centenarian who apparently had foreknowledge of the Ceph and had spent most of the previous century using stolen Ceph technology to design the Nanosuit to be used as a defense against the aliens. Hargreave directs Alcatraz to another Ceph spire to conduct an important experiment for him.
On the way to the spire, Hargreave reveals to Alcatraz that the Manhattan virus had been spread by the Ceph as a method to clear out the entire human population from Earth, comparing it to the previous century's BSE outbreak. The Manhattan virus would cause all infected humans to eventually melt down into a liquidated mass of biological tissue, which could then be easily stored and disposed of. Upon reaching the alien spire, Alcatraz enters it to test whether the Nanosuit's systems can interface with the aliens' technology. The experiment fails, due to the Nanosuit not being powerful enough to ensure the insertion. In the meantime, the US Department of Defense rescinds the authority of CELL over Manhattan and deploys US Marines in their place under the command of Marine Colonel Sherman Barclay. They then attempt to drown the aliens out of lower Manhattan by ordering an air strike on the city's flood barrier. Washed away by the resulting wave of water, Alcatraz is later found in Madison Square Park by a squad of Marines led by Alcatraz's squadmate Chino, who survived the submarine's destruction. The Marines enlist his aid in evacuating civilians to Grand Central Terminal, the city's primary evacuation point.
Hargreave contacts Alcatraz and reveals that the Nanosuit is busy analyzing the alien tissue samples that Alcatraz had previously recovered and is currently rewriting its own code to interface with alien technology. He tells Alcatraz and his marine allies to take a detour to the Hargreave-Rasch building. There, Alcatraz is told to find a stabilizing agent in the bio-lab to facilitate the Nanosuit's analyzing process. However, rogue sections of CELL security in the building still slow down Alcatraz's progress. The Hargreave-Rasch complex is attacked by a Ceph "pinger" robot and is completely flooded, washing Alcatraz out of the building and leaving him unable to enter the bio-lab. Seeing that the cause is lost, Hargreave tells Alcatraz to regroup with the marines at Grand Central to help evacuate civilians. At the terminal, Alcatraz is reunited with Gould, who had apparently "escaped" Strickland, leading to the skepticism of Colonel Barclay. Knowing that Strickland is an ex-Navy SEAL, Barclay concludes that Strickland released Gould from captivity. Grand Central Terminal is overrun by Ceph forces, but Alcatraz manages to hold them off long enough for the evacuation trains to depart, and escapes the building's destruction.
Due to the hasty and incomplete evacuation from Grand Central, Alcatraz is then tasked with defending a secondary evacuation point at Times Square, when another alien spire rises from the ground. By this time, the Nanosuit had sufficiently processed the alien spores, and Alcatraz manages to enter the spire, allowing his Nanosuit to interface with it and re-purpose the spores to be lethal to the Ceph. This causes a cataclysmic self-destruction of the Ceph in the area, and apparently removes all traces of the biological warfare agent. With the evacuation from Times Square complete, Gould instructs Alcatraz to make his way to Roosevelt Island. There, Alcatraz is told to infiltrate a Crynet complex named "The Prism", where Hargreave resides. Alcatraz foils Commander Lockhart's attempts to ambush him, and kills the commander in the process. As Alcatraz makes his way through the island, he is suddenly captured by Hargreave, who wants the Nanosuit for himself so that he can finish off the Ceph personally. Hargreave then attempts to remove the Nanosuit from Alcatraz's body. However, the Nanosuit rejects its removal from Alcatraz since it had already completely assimilated with its wearer, revealing memories of Prophet's fallout with Hargreave in the process. Alcatraz is saved by Strickland, who reveals herself to be an undercover CIA operative, and was responsible for ordering Alcatraz's original mission to extract Gould. Strickland tells Alcatraz to capture Hargreave, but upon entering Hargreave's private office, Alcatraz instead sees Hargreave's body in a vegetative state. Hargreave reveals to Alcatraz that the entire time, his consciousness had been communicating through an advanced computer system, and that this had been the only way for him to communicate ever since he was injured in an encounter with the Ceph at Tunguska. Hargreave gives Alcatraz a last Nanosuit upgrade, the "Tunguska Iteration", before the Ceph invade the island. Hargreave triggers a countdown timer for the self-destruct system of the complex, and orders the remaining CELL forces guarding the Crynet Prism complex to aid Alcatraz's exfiltration. Alcatraz barely escapes the massive explosion of the complex, which destroys much of Roosevelt Island and the Queensboro bridge . On the shores of Manhattan, Alcatraz reunites with Gould, Strickland and Chino.
Alcatraz is notified by Colonel Barclay that the Us Department Of Defense plans to launch a Nucler strike on Manhattan Island with little regard to collateral damage and nuclear fallout . Alcatraz and his comrades make their way through the city toward the center of the alien infestation, and spot a massive alien "litho-ship" rising out of the ground beneath Central park , lifting a large section of the park into the air. With the peripheral aid of Gould, Strickland, and Barclay, Alcatraz assaults the floating section of Central Park, where he has a 20 minute window to end the conflict with the Ceph before they launch the nuclear missile, and succeeds in making his way to the alien spire at its center, which serves as a massive dispersal point for the alien spore bio-weapon. He enters the spire, and his Nanosuit is able to repurpose the spire's bio-weapon to turn against the Ceph. The Ceph in the entire city becomes completely eradicated by self-destruction. After several days, the city begins to recover with the help of Gould, Strickland, and the US Military. Alcatraz, while unconscious, communicates with Prophet, whose memories, experiences, and personality had been stored in the suit. Prophet tells Alcatraz that, while the mission in New York is a success, their work is not yet over since the Ceph, who had been present on Earth since prehistoric times, had built constructs globally that were not only limited to New York and the Lingshan Islands. The Nanosuit then assimilates Prophet's memories into Alcatraz. Upon waking up in Central Park, Alcatraz receives a broadcast from Karl Ernst Rasch, the other founder of Hargreave-Rasch Biotechnologies, asking for his name. Climbing out of the crater, Alcatraz, speaking for the first time since donning the Nanosuit, responds, repeating the same phrase as Prophet, in the beginning of the game: "They call me Prophet."