In 2020, an American team of archaeologists are taken captive by the North Korean Army, just as they were making an important discovery in the South China Sea. The United States responds by deploying a team of Spec Ops who take part in the fighting between the United States and North Korea. This special team were wearing Nanosuits (Also known as Nano-Muscle Suits) Soon, though, it becomes apparent that the North Koreans have large military installations. During this phase of the game, the setting is a tropical environment, similar to that in Far Cry, Crytek's previous game. Early on in the game, it becomes clear that the Korean People's Army KPA isn't the most dangerous threat, as members of the special forces teams starts to get dragged into the deep jungles, later to be found dead. When the spec-ops leader Prophet gets captured by the unknown force and there's only two members left in the special forces team, the United States army enters the scene to fight off the Koreans, but soon find themselves also fighting an unknown alien species.
After the end of the first part, the mountain at the center of the island begins to collapse revealing a 200m high unknown alien structure beneath the surface, out of which aliens begin to attack the US Military and Koreans. Nomad (The lieutenant of the Spec op team) enters in the alien ship and begins to explore the rough environment, returning with valuable information about the alien attackers. On exiting, the ship xeno-forms the area around the island by creating an sphere, inside which the temperature is -200 degrees celsius, flash freezing and killing every living thing, with the exception of those who were wearing nanosuits. (Prophet was also found trapped within the sphere, but his suit was damaged and losing heat quickly. Nomad has to escort him from heat source to heat source to periodically reheat the nanosuit).
Nomad escapes the island, and makes his way to the USS Ship. On board, the admiral reveals that he has permission to start a nuclear assault on the island in an attempt to wipe out the aliens. At this time, Prophet steals a VTOL and returns to the island to fight the aliens. However, the nuke, upon detonating on the surface of the sphere, only gives it more power, and it expands and an army of aliens arrive to attack the USS Ship. The final battle of Crysis 1 takes place against a giant alien warship on top of the ship. Nomad destroys the alien ship, causing it to crash onto the USS Ship, sinking both into the sea. Nomad manages to jump-ship onto the VTOL transport with Pyscho and Helena Rosenthal on it. Shortly after this, a radio transmission from Prophet is received & Nomad insists upon going back to the island to join him.
In Crysis Warhead Psycho is capturing a nuclear material container which contains an alien (It is disabled). Most of the game centers around attempting to capture this box and bring it out of the island. It changes hands many times between Psycho and Colonel Lee (KPA) throughout the game until, finally, at the end, Pscyho and Sean 'O' Neill bring it off the island on a VTOL apparently without pursuit.
In 2023, three years have passed since Crysis, the game begins with news TV show of a large outbreak of the Manhattan virus, a macabre disease that causes complete cellular breakdown, and panic about an alien invasion. 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.
A US Marine Corps Force Recon unit is deployed to New York City by submarine to pick up Crynet employee, Doctor Nathan Gould, who have vital information to defeating the aliens. However, insertion goes wrong, with the Cephaloids destroying the subs, and Force Recon Marine "Alcatraz" being left as the only survivor. Delta Force officer Prophet saves Alcatraz, and is distressed with the situation, expecting the squad to support him. Left with no other choice because he was infected by the Manhattan virus, Prophet gives Alcatraz his suit (Nanosuit 2.0). He then kills himself so that the Nanosuit will stop associating itself with him and be able to assimilate with Alcatraz. Assuming in that suit is Prophet, Gould asks him to take the Marines to his laboratory. but he 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"). Because of this, Alcatraz also fights CELL operatives, who believe that he is Prophet because of his Nanosuit. 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. Gould asks that he head for the crash site and search for any alien tissue samples. Alcatraz is unsuccessful, and the crash site is attacked by a Ceph soldier. Alcatraz kills it and manages to gather alien tissue from its corpse, which causes some sort of reaction within his Nanosuit. Alcatraz meets up with Gould only to be met with initial hostility when he finds out that he is not Prophet. However, when the suit plays Prophet's last recorded message, Gould relents and informs Alcatraz that because of the reaction to the alien tissue, or "Nano Catalyst", the Nanosuit's deep layers may contain a solution to stop the Manhattan virus and combat the Ceph. Gould and Alcatraz commit to further scans at a Crynet base on Wall Street, and 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 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 the building, the Ceph attack the CELL personnel and a massive alien spire rises from underneath the Crynet building, releasing a spore based bio weapon 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 brought upon by the spore bio-weapon. The suit is rebooted remotely by Crynet director Jacob Hargreave, a centenarian who apparently had knowledge of the Ceph and spent most of the previous century designing the Nanosuit from stolen Ceph technology as a defense against them. Under Hargreave's orders, Alcatraz enters one of the alien spires 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 Barclay. They then attempt to drown the aliens out of lower Manhattan by ordering an air strike on the city. Washed away by the resulting wave of water, Alcatraz is later found by Marines, including his Marine comrade 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.
Alcatraz sees 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, an office building of Crynet's parent company, Hargreave-Rasch. There, Alcatraz is told to find a stabilizing agent in the bio-lab to facilitate the Nanosuit's analyzing process, but CELL operatives guarding the building under the command of Lockhart still believe that Alcatraz is Prophet, and attempt to kill him. 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 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 finished processing 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 removes all traces of the biological agents. Alcatraz makes his way to Roosevelt Island to infiltrate a Crynet complex named "The Prism", where Hargreave resides, and manages to kill Lockhart, but is captured by Hargreave, who wants the Nanosuit for himself and attempts to remove the Nanosuit from Alcatraz's body. However, the Nanosuit rejects its removal since it had already completely assimilated with its wearer, revealing memories of Prophet's fallout with Hargreave. Alcatraz is saved by Strickland, who reveals herself to be an undercover CIA operative and ordered Alcatraz's deployment. Alcatraz attempts to capture Hargreave, but Hargreave reveals that he has been in a vegetative state for over a century since an encounter with the Ceph at Tunguska, and that Hargreave's consciousness is only able to communicate and interact through the use of an entirely computerized system. He gives Alcatraz a last Nanosuit upgrade, the "Tunguska Iteration", before the Cephaloids invade the island. Hargreave triggers a countdown timer for the self-destruct system of the complex, and convinces the remaining CELL forces to aid Alcatraz's exfiltration. Alcatraz barely escapes the massive explosion, which destroys much of Roosevelt Island and the Queensboro Bridge. On the shores of Manhattan, Alcatraz meets Gould, Strickland and Chino.
Alcatraz is notified by Colonel Barclay that the US Department of Defense has decided to launch a Tactical Nuclear Strike on Manhattan Island, with little regard to collateral damage. Barclay warns Alcatraz that unless he can come up with a better plan, the strike would likely be carried out despite the risk of dangerous nuclear fallout. A massive alien spire appears in Central Park, and lifts much of the park into the air. With the peripheral aid of Gould, Strickland, and Barclay, Alcatraz assaults the floating section of Central Park and succeeds in making his way to the central alien spire. He enters the spire, and his Nanosuit, with the Tunguska Iteration upgrade, is able to repurpose the spire's bio-weapon to turn against the Ceph, killing all Ceph in New York in the process. Alcatraz, while unconscious, communicates with Prophet (whose memories, experiences, and personality had been stored in the suit), who states that, while the mission in New York is a success, they have more work to do, since the Ceph had ancient constructs built all over the world, and were not only limited to New York and the Lingshan Islands. The Nanosuit, before rebooting again, states assimilation complete, and Prophet's memories are now "assimilated" into Alcatraz. Upon waking up in Central Park, Alcatraz receives a broadcast from Karl Ernst Rasch, the other founder of Hargreave-Rasch, asking for his name. Climbing out of the crater and speaking for the first time in the game, Alcatraz responds "They call me Prophet".
In 2047, nearly a quarter century after the events in Crysis 2, Prophet returns to New York and discovers the corrupt private military corporation, CELL, has erected a giant Nanodome over the city. Destruction and decay have allowed Mother Nature to reclaim much of the metropolis, aided by the dome that has caused a greenhouse effect; crumbling buildings now house winding tree trunks, railroad tracks are covered by tall foliage and dense swamps snake between boroughs. This striking contrast serves as a backdrop to your "revenge mission" against CELL. Prophet's personality, stored in his Nanosuit, assimilates and takes control over Alcatraz's body. Joining with Psycho and a team of elite Nanosuit soldiers, he travels around the world looking for the Alpha Ceph from the knowledge he gained about Ceph existence during the events at Lingshan. One by one his team loses interest in the hunt believing that all Ceph are destroyed, until Prophet and Psycho finally trace the Alpha Ceph in Siberia, Russia, only to be disabled by CELL using K-Volts. CELL, now in search for global domination of land and technology, betrays all the remaining Nanosuit soldiers and starts skinning the suit out from their body so as to recover the lost alien technology. Everyone involved in the Nanosuit program were either recruited or detained by CELL, including Scientists Nathan Gould and Claire Fontanelli. CELL runs out of Nanosuit soldiers to skin for alien technology that integrated with their suits, so the transfer of Prophet to the facility was requested. Locked in a storage device with powerful EMP shocks to keep him dormant, Prophet is transported to the nanodome in New York by CELL.
However, Karl Ernst Rasch comes to know about the corrupt intention of CELL and resigns from the post of CEO of Hargreave-Rasch Biotechnologies, deletes all the research done by him and Hargreave of Ceph Technology so as to stop CELL from acquiring it and secretly releases a brief video of Prophet's where-abouts, also describing the post scenario after the invasion of New York and the evolution of Ceph, thus requesting the resistance to free Prophet as only he can stop the CELL and put an end to their corrupt motives and then joins the resistance. Members of the resistance, including former nanosuit soldiers Psycho, Lazy Dane and Bandit, are able to free Prophet from the transport ship, which has docked at the New York nanodome.
Psycho explains that in Prophet's 20 year absence, CELL used Ceph technology to generate unlimited free energy. Eventually, CELL gained a monopoly over the power supply, and used it to drive everyone into debt. Those who could not pay were sent to "volunteer camps." A resistance movement formed in response to this. It eventually freed Psycho from the skinning labs, and he joined their ranks. Tara Strickland from Crysis 2 also helps the resistance politically as a senator, but is unable to do much due to CELL's political dominance. The source of CELL's power generation for the entire world, called System X, is also located in the abandoned and encased New York, which has grown into a jungle. Psycho wants System X destroyed to free the world from CELL. Prophet, though worried about his visions of the Alpha Ceph showing him the end of the world, agrees.
Psycho and Prophet enter the dome, fighting through CELL forces and feral Ceph Stalkers. They reach the resistance headquarters, where they meet Karl Ernst Rasch and Claire Fontanelli, the commander of the resistance. Rasch tries to convince her that Prophet is what the resistance needs to finally overthrow CELL. Despite affirmations from Psycho, with whom she seems to have a special relationship, Claire is skeptical of Prophet, ostensibly because of the extensive modifications, the integration of Ceph genetic material, and the deep integration with his suit. Grudgingly, she eventually agrees.
Their first target is System X's outer defenses. Despite CELL's capacity for infinite power generation, CELL chose to power its defenses with a hydroelectric dam. Prophet hypothesizes that CELL does this because it fears something about System X. Prophet, who continues to have visions, disables the dam and then disables the System X facility. It is revealed that System X is the Alpha Ceph. A system program designed to kill the Alpha Ceph when necessary activates, but fails, and the facility self-destructs. The Alpha Ceph fires a beam into the atmosphere to open a wormhole to the Ceph home world in the M33 Galaxy. Through this wormhole, they plan to send an invasion force to invade the planet, revealing their true motives for inhabiting the planet for millions of years. The Ceph mind reactivates, and a coordinated Ceph attack begins. Prophet resolves to kill the Alpha Ceph and end the threat once and for all.
Prophet learns that he must unlock his suit to defeat the Ceph. Prophet and Psycho head to the skinning laboratory to use the cradle to do this and to find out who was responsible for skinning Psycho. At the facility, they see firsthand the atrocities visited upon the Nanosuit soldiers by CELL. Psycho uses the cradle to remove the neural blocks put in place to prevent the Ceph from taking over Prophet's mind. It also lifts the restrictions on the nanobots in Prophet, and they are now able to transform. Meanwhile, Psycho does more digging into his past, despite orders from Claire. He discovers that it was Claire who had skinned him and the others at the behest of CELL. Upset, he rebuffs efforts from Claire and Prophet to console him. Claire pleads that he was the reason she joined the resistance, and that she had no other choice. Prophet also claims that he had no other choice, and that he told him what he needed to know at the time of the Lingshan Incident. Psycho finds this unacceptable, as everyone has a choice. He hands Prophet the dogtags of Nomad, Aztec, and Jester, and leaves.
Prophet learns that because the Alpha Ceph is creating a wormhole, the CELL plans to use Archangel, a satellite based energy distribution platform that can draw power from the entire world's power grid, as a directed energy weapon to destroy all of New York and hopefully the Alpha Ceph. Unfortunately, firing it at the Alpha Ceph would cause a chain reaction that would destroy the whole planet. To make matters worse, the Ceph attack Claire and the resistance. Prophet rescued them, but the situation is so horrible that Claire tells him to leave them, as they are only holding him back. Psycho shows up with a VTOL and rescues the resistance. They proceed to the Archangel control facility where they shut off the weapon before it unleashes enough energy to set off a chain reaction. Rasch, who had used Ceph DNA to extend his lifespan, is recovered in the facility, but is now under the control of the Ceph. He disables Prophet and tries the same on Psycho, but Claire blocks his attack and Psycho shoots Rasch. No longer under control, Rasch implores the group to leave as the Ceph tentacle renews its attack. Prophet, Psycho, and the injured Claire board the VTOL and engage in a massive air battle, eventually crashing. Claire, succumbing to her injuries, is forgiven by Psycho and dies. Psycho laments to Prophet that he is powerless because he does not posses a Nanosuit. Prophet fights with Psycho, revealing that Rasch had incapacitated Prophet because of his integration with his suit, and that they only survived because of Psycho's humanity. Psycho, now going by his human name Michael, resolves to do the slaughtering and procures another VTOL to take the battle and Prophet to the Ceph.
Michael and Prophet kill the Alpha Ceph, destroying the wormhole device, but the beam powering the wormhole pulls Prophet into space. Now in orbit, Prophet sees a massive Ceph Ship, similar to the one in Lingshan, coming through the wormhole. His suit heavily damaged, Prophet almost gives up, but instead he pushes on. Recalling Archangel's immense power, Prophet hacks into the satellite and uses it to destroy the Ceph ship. This collapses the wormhole and ends the threat of invasion. In the explosion, Prophet is knocked off the satellite by debris and falls back to Earth. He impacts the water in Lingshan Island where 27 years ago the Ceph were initially discovered. When Prophet wakes up, he is in a house in Lingshan. In the background, there is a news broadcast of the now Senator Tara Strickland, who announces that the remaining assets of the CELL corporation have been seized as part of the global recovery effort. The Nanosuit, now more symbiotic than ever before, changes its outer layer to resemble a human body, and restores the original face of Prophet, thus technically resurrecting him as he grabs the dogtags of his deceased Raptor Team squad members, thinking how much he sacrificed his humanity and his body in his quest for victory. He walks out to the beach, throws the tags into the water, and deciding to use his actual name "Laurence Barnes" from now onwards, walks back towards the house, cloaks repeating his famous taglines "They called me Prophet. Remember me." Elsewhere, two frightened CELL troopers and three frazzled men hurriedly retreat down a corridor. They are being attacked and pursued by an unknown enemy accompanied by strange sounds. It is revealed that the three men comprise the CELL board of directors. A door closes without incident. The CELL troopers turn around and are shot. The three nervous men turn to find Michael sitting at a desk. He claims to have had spent some time at one of their hospitals, and he wants to file a complaint.
