Prior to the siege, the Cocoon inhabitants were in the grip of Pulsian panic. The Cocoon fal'Cie had manipulated the population into thinking that armies from Gran Pulse would attack Cocoon at any moment, thus the population developed great animosity towards the six Pulse l'Cie. PSICOM and the Guardian Corps divisions, under the orders of Director Yaag Rosch, set out to hunt down and kill them.
One Guardian Corps Division, the Cavalry, under the command of General Cid Raines, saw through the fal'Cie's schemes and sought to search for the Pulse l'Cie in their efforts to liberate Cocoon. However, Raines is later revealed to be a Sanctum l'Cie whose Focus was to set the Pulse l'Cie on the path to destroy Cocoon.
The fal'Cie's true goal is to sacrifice all the Cocoon's inhabitants in order to summon the Maker. However, as they are incapable of doing the deed themselves, they are forced to use a group of humans to carry out the task. Raines leaves the Cavalry and attempts to fight against his Focus and defeat the Pulse l'Cie to prevent them from fulfilling theirs. Raines is defeated, but transforms into crystal, despite not fulfilling his Focus.
While the l'Cie are on Gran Pulse coming to terms with their Focus, Barthandelus, under the guise of Galenth Dysley, resigns as the Sanctum Primarch and appoints the revived Cid Raines in his place. This angers the Cavalry, now commanded by the newly promoted General Rygdea and provokes them into action. The l'Cie encounter Barthandelus in Oerba, who informs them of the Cavalry's plan to destroy Orphan. The Cavalry, thinking that destroying it will liberate Cocoon, will in fact destroy the floating continent. This forces the l'Cie to return to Cocoon with a plan to stop the Cavalry from reaching Orphan.
As soon as the l'Cie arrive in Eden, Barthandelus releases Pulsian monsters from the Arks into the floating city, inciting panic among the populace. Meanwhile, the Cavalry raids the Sanctum headquarters looking for the new Primarch Cid Raines. Raines offers no resistance to the Cavalry, and is reluctantly killed by Rygdea with a single shot at close-range. The Cavalry then make their way to Edenhall, to Orphan.
According to Final Fantasy XIII Gaiden Shōsetsu: Yumemiru Mayu, Akatsuki ni Otsu, the race in Eden is held as a festival celebrating Cid Raines's appointment as the Sanctum's new Primarch. The Cavalry, an elite group of soldiers seeking to free the people from fal'Cie rule, see their leader, Raines, now acting as the voice of the fal'Cie as an act of betrayal. The Cavalry raises an army in response, unknowingly playing into the fal'Cie's hands. As the rebellion breaks out, monsters from Arks hidden in the city are released. Neither the Guardian Corps's Homeguard, tasked with keeping order in Eden, nor PSICOM, stationed in the city as a precaution against the l'Cie, are able to make a move against the mechanical soldiers that were made to combat the biological weapons that survived the process of natural selection that rules Gran Pulse. With the military divided, Eden descends into chaos and everything is sent down the path to destruction.
The l'Cie head to Edenhall and fight through the Sanctum and Pulsian forces. They are met by Yaag Rosch, who fights the party with the Proudclad. The l'Cie defeat Rosch, who retreats.
As the l'Cie fight their way through to the Edenhall's front gate, they are met with a strange phenomenon. The air is filled with floating crystal shards, marking the appearance of Etro's gate as Barthandelus intended to occur. Thinking it signifies Cocoon's suffering, they press on into Edenhall, but are shocked to witness the Sanctum forces and the Cavalry soldiers transforming into Cie'th, and Yaag Rosch, the sole survivor, attacks the party again in the Proudclad.
The l'Cie eventually destroy it and the mortally wounded Rosch finally comes to the conclusion that the fal'Cie are Cocoon's enemies and implores the l'Cie to stop them. Rosch commands the Sanctum forces to suspend l'Cie operations and focus on civilian evacuation; he then sacrifices his life to stop the approaching Behemoths from attacking the l'Cie as they descend into Orphan's Cradle.
The l'Cie, through the help and guidance of the fal'Cie Eden, approach Barthandelus for the final time in the Narthex. The l'Cie fight Barthandelus and defeat him. However as the l'Cie begin celebrating, the fal'Cie Orphan appears after having absorbed Barthandelus's body. Orphan wishes its own death and forces the l'Cie to fight it, resulting with all but the Oerbans becoming Cie'th, and Oerba Yun Fang willingly becomes Ragnarok.
However the process is not complete as Fang is unable to destroy Orphan. Orphan tortures Fang for her failure in a cycle of pain and healing, goading her to become Ragnarok and be fully consumed in rage and finish the job she failed to accomplish five-hundred years prior. Suddenly the Cie'th transform back into l'Cie, having realized their transformation to be a fal'Cie illusion, and destroy Orphan's shell to stop Fang's torture.
The party fight Orphan's true form and defeat it, ending fal'Cie domination, with Vanille and Fang sacrificing themselves to become Ragnarok together, and saving everyone in Cocoon while Etro's gate fades away.
With Cocoon now trapped in crystal, its now-former inhabitants migrate to Gran Pulse to begin new lives on the surface world. Goddess Etro takes pity on Lightning, Snow, Hope, Sazh, Serah, and Dajh and, inspired by their courage and bravery, frees them from being l'Cie.