After the events of Crysis 2, Prophet and Psycho track the Alpha Ceph to Russia and imprison it. Then CELL Corporation moves in — capturing all Nanosuit soldiers and stripping them of their suits to harvest the Ceph genetics inside. Prophet is taken to a dome facility in New York, where a resistance cell led by Claire Fontanelli and Karl Ernst Rasch breaks him out. CELL has used Ceph technology to monopolize the world's energy supply, and the resistance wants System X — the source of that power — destroyed. What follows involves the Alpha Ceph breaking free, a wormhole to the Ceph homeworld, a satellite weapon capable of ending both the Ceph and Earth, and a chain of betrayals and losses that strips the team down to its last members. Prophet ends the threat from orbit, crashes into the ocean near the original Lingshan Islands, and wakes up as himself again for the first time in years.