The l'Cie learn everything was a ruse set up by the fal'Cie who have been manipulating their every action in the shadows. The fal'Cie's ultimate purpose for Cocoon is to be a 'farm' for individual souls, which the fal'Cie wish to expend to summon a god that they call the Maker from the other realm. Trying to protect Cocoon despite it going against their Focus, the l'Cie collect in the fal'Cie Orphan's resting place, the fal'Cie that forces all the other fal'Cie in Cocoon. Since the party sees Orphan shares the other fal'Cie's goal to forfeit the citizens of Cocoon, they conclude there is no way for mankind and fal'Cie to co-exist. The party admits their true Focus is to save Cocoon and kill Orphan. As Cocoon falls from the skies Fang and Vanille summon the mythical monster Ragnarok to erect a crystal pillar to sustain Cocoon above Gran Pulse, and the world is saved.
The members of the team react to their plight in various ways: Snow makes protecting Serah's crystal his priority; Lightning sets upon a path of revenge against Cocoon's governing body, the Sanctum, and all fal'Cie with Hope, who views her as a role model, after suit; while Sazh and Vanille choose to run out of their fate. They know Vanille is harboring a secret of being a l'Cie from Pulse all along, and she and her friend Fang--who joins their team--were involved in the warfare between the two worlds over six hundred years ago, sleeping through the centuries in crystal stasis. After settling their differences the party decides to work together to halt the fal'Cie's plan, and gain the help of a rogue army regiment, the Cavalry, that posits their wish is to free Cocoon from fal'Cie rule.
The principal themes of Final Fantasy XIII are hard fate and the idea of willpower. The main cast has an unfair fate forced upon them and find a way to escape it and do what they believe is right. Ultimately free will triumphs over destiny, since the party rejects their Focus and follows their true desire, to save Cocoon. The themes are found together with the characters of Serah and Cid Raines, who likewise resist their destiny, and with the interactions of Hope and his father, who tells Hope he must find his own path in life. The fal'Cie are on the opposite side of this coin, unable to follow their heart's desire as their destiny is predetermined by their founder.
Cocoon is plunged into chaos when a Pulse fal'Cie is discovered in an old Pulsian landmark in the town of Bodhum. Fearing that anyone that's been in its vicinity might now be a l'Cie servant of a hostile fal'Cie from another planet, Cocoon's governing body enacts a Purge to eliminate everyone who happened to be in Bodhum during the fal'Cie's discovery. At the center of the events is Serah Farron, a local girl who had unwittingly wandered into the vestige and been made a l'Cie and is now held captive by the fal'Cie therein.
Other central topics are theocracy, a system of government that rules under one god known as the supreme ruler, and totalitarianism, a government system in which all elements of life are controlled by the supreme ruler and any resistance is forbidden. After theocracy, Cocoon's Sanctum is led by the fal'Cie Eden that communicates through Primarch Dysley, who acts as Eden's messenger and makes its orders known to the rest of Cocoon. In accordance with totalitarianism, the military forces follow the Sanctum's policies without question and ensure the populace follows suit. They justify their actions by claiming them to be for the greater good of everybody and necessary to keep the peace, willing to go so far as fire upon unarmed civilians who attempt to escape or resist.
Despite lacking magical powers and immortality like the fal'Cie, people are still indicated to be stronger in the end due to possessing free will, and Orphan describes to the party that humans' infinite potential is why fal'Cie chose to make l'Cie of guys to carry out tasks they are unable to do. Having a white l'Cie brand may represent a human's free will triumphing over the bond of a fal'Cie-given Focus, as in the end of the game, each of the party's l'Cie brands burn out, which is known to halt the practice of turning into a Cie'th.