Raptor team (Nomad, Psycho, Prophet, Aztec, Jester) are dropped onto the island to answer a distress signal sent out by U.S archaeologists claiming the KPA had taken over the island and killed some archaeologists. During the drop Nomad is hit by a mysterious creature and the squad is scattered. Aztec and Jester are quickly killed off by the creature's leaving Nomad, Psycho and Prophet left. The situation becomes dire as Prophet himself becomes captured by the Aliens and assumed MIA.
Soon the U.S.M.C announce their intentions to re-take the island and launch an assualt on the KPA defensive line, destroying a Korean frigate and ultimately pushing their way to General Kyong's position in the mountain. Nomad is captured and Kyong (despite warnings) opened the mysterious structure in the mountain thinking it was a new power source, but instead electrical sparks fly out from the structure, allowing Nomad the chance to fight and kill Kyong.
Nomad is then forced to travel through the Alien structure to escape the rapidly collapsing cave, during which he see's many different variants of the Aliens. The situation becomes FUBAR as the Aliens flash freeze the island and engulf part of it in a sphere, freezing everything inside and leaving Nomad the only known survivor. As Nomad attempts to escape the sphere, he is ambushed by a squad of Aliens, only to be saved by the return of Prophet, who somehow survived his abduction earlier on, and managed to modify an Alien weapon for Human use. Nomad escorts Prophet out of the sphere, and the overwhelmed U.S forces begin to evacuate the island, losing the Marine Commander, Major Strickland in the process.
After evacuating the island, the call goes through to launch a nuclear strike at the island. Just as the strike is authorised, Prophet steals a VTOL and goes back to the sphere and is presumed dead after the nuke detonates. The nuke failed to destroy the sphere, instead empowering and causing it to expand, prompting the Aliens to launch an all out assault on the U.S fleet. Nomad attempts to defend the Carrier as wave after wave of Alien's assault the ship. One by one the fleet begins to fall until only the Carrier is left. Eventually, after fending off a couple of waves, an Alien Warrior (Massive warship about the size of an Aircraft carrier) assaults the Carrier. With the help from Psycho and Helena, Nomad destroys the Warrior and evacuates on a VTOL flown by Psycho.
Word comes in of a fleet from Japan on its way to the island. However, Psycho receives a transmission from Prophet who is somehow still alive and Nomad orders them to return to the island, as an armada of Aliens are pouring out of the mountain to begin the onslaught on humanity...
Fast forward 3 years, the events of Crysis 2 begin. Hope this helps anyone who hasn't played the original Crysis understand how the Aliens were discovered and gives anyone a better understanding of the story in Crysis 2