The plot focuses on the fal'Cie, beings created from the crystals residing inside them. The people marked by the fal'Cie for a greater purpose are named the l'Cie. But being a l'Cie has a price; for should they die before fulfilling their Focus, they will turn into monsters called "Cie Corpses". Some thirteen centuries ago, a fal'Cie constructed a paradise for humanity: The shell-like city of Cocoon floating high above the surface of the world now known as Pulse, both maintained by their own fal'Cie. Cocoon's fal'Cie created life forms and machines for its inhabitants to use, and humanity flourished. Over time, the people of Cocoon began to fear for the safety of their world, and were worried that it would be cast down from the sky into the hell that they see Pulse to be.
In present day, the wilderness of Pulse has strange effects on people, and the theocratic Cocoon Sanctum quarantines and exiles anyone who has been influenced by Pulse from the city with the help of its mighty army, PSICOM. However, as Snow leads Team Nora in a vain attempt to stop the purging, the mysterious Lightning fights her way past PSICOM soldiers to find Pulse's fal'Cie with the aid of Sazh. But by a chain of events, these three along with two of the Purgees, Vanille and Hope, are chosen by the fal'Cie of Pulse against their will to become l'Cie among others, and with that become enemies of humanity that would bring about the downfall of Cocoon.