Over two decades after the events of Crysis 2, you assume the role of Prophet as he returns to New York, which is now encapsulated in a giant nanodome created by the corrupt CELL corporation. Think Springfield in The Simpsons Movie but with fewer Spider-Pigs.
Cut off from the outside world, New York has been turned into a jungle, reshaped by mother nature reclaiming what she’d lost before man built over it all. This has led to seven distinct environments within the zone, known as the Seven Wonders. But who built these nanodomes and why? The population of New York was told it was for their protection from the remaining Ceph left behind from the events of the last game but the real reason CELL built them was to aid them in their quest for global domination. And who’s going to stop them? Why, us of course!