Crysis is a 6-issue series intended to bridge the gap between the storylines of Crysis and Crysis 2. The story focuses on the adventures of Prophet, Nomad, Psycho, and Helena Rosenthal. It also reveals much of Prophet's backstory. The comics are also intended to be released as a single graphic novel on January 31, 2012.
While waiting to be rescued, Prophet fights off wave after wave of Ceph. Interestingly, the Ceph are equipped with exoskeletons similar to those in Crysis 2, though there are some that aren't in either game. The ice sphere also seems to have disappeared. It is revealed that Prophet was on the verge of being dishonourably discharged and sent to Leavenworth before testing the Nanosuit. He also becomes quite fond of his Nanosuit, comparing it to a "second skin". Unfortunately, the VTOL, his evacuation, gets shot down as it approaches.
As the survivors leave the downed VTOL, it is destroyed by a giant bipedal Ceph. Everyone is knocked down and Nomad is severely wounded in the process. Prophet comes to their rescue and defeats the giant Ceph and other attackers with grenades and a heavy weapon. Nomad recovers quickly due to his Nanosuit. When they get to safety, Prophet explains that the mission was nothing but a cover for Jacob Hargreave's agenda, much to everyone's shock. He also reveals that he was nearly dishonorably discharged and imprisoned for assaulting his CIA advisors and commanding officers, due to his disagreement with their unethical methods in the War on Drugs. Psycho agrees, saying that he would have done the same thing himself. Prophet then reveals that Jacob Hargreave was the reason for his release and subsequent participation in the Nanosuit program.
Prophet tells Helena and the rest of his team how Hargreave saved him from Leavenworth, and how everything he said turned out to be true. While Helena and Psycho were sympathetic, Nomad is very uncomfortable with the fact that Prophet is a "private-sector mole".
Hargreave then contacts Prophet about a private vessel still docked on the opposite side of the island, and Psycho is outraged that he's fighting "squid" and "calamari". The team is told that if they are picked up by the military, they will likely be interrogated by a third party that's neither Army nor C.E.L.L. While making their way over to Hargreave's vessel, the survivors decide to take a shortcut through the alien ship, which no longer has an anti-gravity field. Unfortunately they're discovered by the Ceph inside and they're forced to step through what appears to be a portal, one that Prophet would rather not have to go through.
Meanwhile, Vice-Admiral Sanchez meets with some people who want to extract Raptor Team for classified reasons.
Helena Rosenthal and the remnants of Raptor Team are transported to one of Jupiter's moons. None of them could believe what they were seeing, and the Ceph did not follow them through the portal. Though Helena speculates that the Ceph may not have built the portal, Prophet likens it to programming parameters preventing himself and Psycho from capturing a terrorist years ago in Kuala Lumpur, when he escaped into an embassy.
Nomad, however, is much more focused on the mission at hand and wants to know how Prophet survived and managed to acquire an alien weapon the first time he went through the portal. Prophet explains that the Nanosuit is based on technology stolen from the Ceph, and that the Scout was only trying to connect with Aztec and Jester when it killed them. Jester wasn't killed immediately like Aztec was, and it took even longer in Prophet's case, giving him time to stab the Scout and repel it. However, he was left inside a cave and attacked by tentacles, which nearly caused the cave to collapse and bury him. After he escaped, he found a surviving North Korean Army Captain, Pak, whose squad was massacred by the Ceph inside the structure. After accusing each other of stealing Nanosuit technology, Pak revealed that General Kyong's unit has been training with Nanosuits for a long time, and that it's likely that each military developed their suits separately. According to Pak, Korean Nanosuit soldiers dream of the structure inside the mountain, but Prophet denies that he does too. Pak then reveals that the Nanosuits started giving soldiers bad effects ever since they came to Lingshan.
After Prophet rescues Pak from an attack by the tentacles, they step into a zero-G area and are attacked by the Ceph again.
Eventually, Prophet and Pak are overwhelmed by the tentacles. Pak sacrifices himself with a grenade, killing the tentacles and sending Prophet through the portal, where he finds an ancient alien that died for an unknown reason, without firing a shot. Inspired by the dead creature, Prophet leads the survivors back through the portal.
It is revealed that the portal sent them back through time, where they can hear themselves fighting the Ceph 18 hours ago. Prophet then reveals that he even saw himself talking to Pak after he came out of the portal the first time. It also seems to be why his Nanosuit was malfunctioning, though it managed to fix itself eventually. The survivors continue on to the shore, where they called for Hargreave's boat. Prophet contacts his old self as well, to ensure that events play out exactly the same way.
As the boat arrives, the crew opens fire on the survivors and takes them by surprise. Helena, who isn't wearing a Nanosuit, is killed immediately. The boat then disables the Nanosuits with an EMP. As Prophet lies in the sand, he realizes that they've all been betrayed. The boat's crew then prepares to bring them onto the ship for interrogation.
The "evac crew" inspect their victims and find that while Prophet and Psycho are alive and well underneath the locked-up suit, Nomad is badly injured. It is then revealed that they hijacked Hargreave's vessel and killed the original crew so efficiently that Hargreave never even realized the boat's been taken over.
Once on board the boat, Norman West, the CIA officer that Prophet beat up in Panama, reveals himself to the captives, saying that this was for revenge against Prophet. He then proceeds to beat up Psycho, who is still unable to move. Prophet becomes exasperated at the fact that the CIA has no clue as to what's really going on, pointing to the aliens on the island. West then has his men injure the unconscious Nomad with a drill, forcing Prophet to tell them the coordinates for Hargreave's bunker in exchange for Nomad's life.
As Prophet expected, however, the boat is hit by an EMP blast released from Morrison's nuke. Prophet and Psycho break free and start killing their captors. However, one of West's men attempts to kill them with a rocket launcher. Nomad bursts through the wall and takes the hit, sacrificing himself for his teammates, who then kills the rest of the crew. Prophet terminates West with extreme prejudice. After mourning the loss of Nomad, the two surviving members of Raptor Team decide to take their data to Hargreave and seek refuge there.