It seems the aliens uncovered by Crysis' nanosuit-wearing Prophet and friends have evolved, gunned up, and have come to fight for their rights to the planet - they are the Ceph. Throw into this the machinations of a few corporations, a flesh-eating virus and a nerdy computer programmer, and you've got a plot that makes little sense until towards the end - but that's hardly an issue, as the rest of the game is awesome.