Up to 16 players on the PC and 12 players on consoles are supported in each multiplayer match, which uses the Origin client and requires the user to have an existing user account or otherwise create a new one. It works with servers. There are 8 different modes and 6 modifiers, each with 12 available maps
Players take on the role of Prophet as he returns to New York in 2047, 24 years after the events of Crysis 2. He discovers the city has been encased in a giant Nanodome created by the corrupt CELL corporation. The New York City Liberty Dome is a veritable urban rainforest teeming with overgrown trees, dense swamplands and raging rivers. Within the Liberty Dome, seven distinct and treacherous environments become known as the Seven Wonders. Prophet is said to be on a "revenge mission" after uncovering the truth behind CELL's motives for building the quarantined Nanodomes. The citizens were told that the giant citywide structures were erected to protect the population and to clean these metropolises of the remains of the Ceph forces. In reality, the Nanodomes are CELL's covert attempt at land and technology grab in their quest for global domination by means of debt enslavement.
After the events of Crysis 2, Prophet's personality and memories stored in Nanosuit assimilates with Alcatraz's body along with Alcatraz's memories, 'like a spare ghost part' in the process. Prophet now knows that he died by shooting himself and is now back from the memories stored in the nanosuit (which is shown in the flash videos in-between). 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. One by one his team loses interest in the hunt believing that all Ceph are destroyed, until Prophet and Psycho finally traces the Alpha Ceph in Russia and imprison it. CELL, now in search for global domination of land and technology disables Prophet using powerful K-Volts in Siberia, captures all the remaining Nanosuit soldiers by corrupt tactics 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. But 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 New York, now encased with giant "nanodome" by CELL.
However, Karl Ernst Rasch by using Ceph technology had extended his life and comes to know about the corrupt intention of CELL. He resigns as the head of Hargreave-Rasch Biotechnologies, removes all the research done by him and Hargreave on Ceph Technology to stop CELL from acquiring it and secretly releases a brief video of Prophet's where-about, describing the post scenario conditions after invasion of New York and the evolution of Ceph, thus requesting the resistance to free Prophet as he is the only Nanosuit holder left who can stop the CELL and put an end to their corrupt motives. He then himself 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. The New York Nanodome, dubbed 'Liberty Dome', which is now full of overgrown trees, vegetation and with reasonable wildlife. The building of nanodome was to keep the city non-functional and to keep people away. 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 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 power production core called Nexus facility. It is revealed that System X is the Alpha Ceph. A system program designed to contain the Alpha Ceph when required, activates but fails, leading to the initiation of secondary defence protocol causing the facility to implode and self destruct. The Alpha Ceph as it is free now enables a ceph structure inside the nanodome to fire 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 inhabitating the planet since millions of years. The Ceph hivemind also know as mind carrier, Alph Ceph or Ceph Tentacle reactivates, and a coordinated Ceph attack ensues. Prophet resolves to kill the Alpha Ceph and end the threat once and for all.
Prophet learns that he must unlock his suit to its full potential by removing the neural blocks, to defeat the Ceph. Prophet and Psycho head to the skinning laboratory to use the cradle to do this and inadvertently discover 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 nanites in the suit. The nanites will be now able to transform into anything as it as no limitations. 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 the men that died under his command, Aztec and Jester during the original Crysis and Cupcake during the Alpha Ceph hunting mission between Crysis 2 and 3, and leaves.
Prophet learns that it because of the reason the Alpha Ceph is controlling the ceph structure for 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 races to rescue them, but the situation is so dire 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 Alpha 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 Alpha Ceph also know as 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 was only able to incapacitate Prophet because as he was wearing the nanosuit, and that they only survived because of Psycho as he was not wearing a nanosuit. 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, which is controlling the Ceph Structure from which the wormhole is beaming from. As they only destroyed the Alpha Ceph and didn't have enough time to destroy the Ceph Wormhole Structure which is now completely functioning, 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 Archangel 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 by the debris and is pushed back into the earth's atmosphere. He impacts in the waters near Lingshan Island where 27 years ago the Ceph were initially discovered. When Prophet wakes up, he is in a abandoned hut in Lingshan. In the background, there is a news broadcast of the Senator Tara Strickland who announces that the remaining assets of the CELL corporation have been frozen and seized as part for the global recovery effort. As the neural blocks now removed from the Nanosuit to destroy the Alpha Ceph, the nanites in the suit can rearrange to anything unimaginable, making the nanosuit more symbiotic than ever before. It changes it's outer layer as a human body and restores original face of Prophet, thus technically ressurecting him as he grabs the dogtags of his deceased squad members thinking how much he sacrificed his humanity and his own body in the 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.