The story of Lightning Returns: Final Fantasy XIII takes place 1000 years after the events of Final Fantasy XIII and 500 years after Final Fantasy XIII-2 in the world of Nova Chrysalia. It focuses on Lightning who works as the savior to save the souls of humanity before the end of the world.
In the year 1000 AF, five hundred years after Chaos entered the mortal realm, Lightning awoke from her crystal sleep in the world of Nova Chrysalia. The world is doomed to be destroyed and Bhunivelze—the god who created the fal'Cie deities: Pulse, Lindzei, and Etro—chose Lightning to be the savior tasked to free mankind's souls and lead them into a new world he is crafting. In return, Bhunivelze assured Lightning he will resurrect her sister Serah.
Lightning teamed up with her former companion Hope Estheim, who has physically regressed to his teenage state. Although he remains in the Ark, the two keep in contact over wireless communicators, with Hope guiding Lightning through knowledge he obtains by analyzing the Chaos around her. Hope tends the tree, Yggdrasil, which acts as a preserving force for the world, extending its life to the maximum of thirteen days in exchange for an energy called Eradia, obtained whenever a soul is saved. After each day Lightning is pulled back into the Ark where she relinquishes the Eradia she has collected from saved souls to the tree, and each new bloom on the Yggdrasil grants one more day for the world.
As Lightning sets out on her quest she encounters many of her former allies. Snow Villiers, depressed over Serah's death and still a l'Cie, has become Patron of the pleasure city of Yusnaan. Noel Kreiss, tormented by his role in Etro's and Serah's deaths and the world's current state, has become a vigilante in the religious city of Luxerion. Oerba Dia Vanille is being sheltered by the Order of Salvation, being hailed a saint for having gained the ability to hear the voices of the dead. Believing the Order is using Vanille to suit their own ends, Oerba Yun Fang leads a band of thieves in the Dead Dunes to obtain a relic the Order is after.
In the Wildlands, an untamed region where the creation of Nova Chrysalia took place, Sazh Katzroy grieves over his comatose son Dajh while Mog leads a settlement of moogles. Caius Ballad, the man responsible for Nova Chrysalia's creation, resides within the ruins of Etro's temple where the Chaos is bleeding from with only the various incarnations of Paddra Nsu-Yeul for company. Lightning also encounters the mysterious child-like entity Lumina, who resembles Serah in appearance, whose agenda is unknown. Every now and then Lumina pulls Lightning into a secluded place apparently existing inside her soul where Hope cannot hear their conversations to plant seeds of doubt in Lightning's mind on Bhunivelze's true plan for her.
In Yusnaan, Lightning storms the end of the world festivities at Patron's Palace to confront Snow, Serah's fiancé and the last l'Cie in the world. As a Chaos infusion manifests inside the palace Lightning aids Snow in dispersing the monsters that emerge from it, but afterward the two turn their weapons on each other, as Snow does not trust her. Lumina intervenes and breaks Lightning's weapon, and Snow retreats deeper into the palace. Lightning follows, but is halted by a locked door. She can sense Chaos on the other side and questions Snow's sanity if he went inside. Lightning retreats as she hears the guards approaching and the day draws to a close.
A cult known as the Children of Etro believes Lightning to be the harbinger of the oncoming Apocalypse, and murders pink-haired women during their nocturnal rites to lure her out. While putting a stop to the cult's activities in Luxerion, Lightning runs into Noel Kreiss who believes he must kill her to ensure the coming of a better world and allow him to reunite with the seeress Yeul from his era, a girl who was endlessly reborn back when time still flowed normally. It turns out the Oracle Drive prophecy he followed is a fake created by Lumina, and when given a chance to strike at Lightning Noel destroys the Oracle Drive instead. Yeul's spirit emerges from the damaged Oracle Drive and promises they will be together soon, and Lightning saves Noel's soul by freeing him from his burden of guilt.
After hearing of Lightning's exploits in the city Vanille requests to see her, and Lightning is granted night time passage into the Luxerion Cathedral after she delivers Vanille's missing crystal shard to her aide. Lightning finds Vanille with Lumina, and the former shows Lightning a mass of Chaos residing underneath the cathedral she dubs the wind of sorrow. After Etro's death the cycle of life was broken with no new life being born, and the dead no longer passing on, instead staying trapped in a state of limbo with Vanille able to hear every cry of their pain. Vanille is determined to help the dead as she is the only one who can hear them, and thus has decided to stay with the Order of Salvation who claims to have discovered a way to save the dead by granting them oblivion as per Bhunivelze's orders. The Order is an organization that acts as de facto world government who worships the god Bhunivelze and spreads the word of the oncoming end of the world and the salvation Bhunivelze has promised his followers in a new world.
Lightning returns to Yusnaan and infiltrates Snow's palace during the performance of the The Song of the Savior show. She proves to Snow she is not an impostor by recognizing the engagement necklace he and Serah wore after deciding to marry. Snow desires death as penance for his failure to protect Serah, and intends to have Lightning kill him after absorbing the Chaos infusion at the center of his palace he has been containing to save Yusnaan. Snow transforms into a Cie'th but is defeated in battle, and Lightning reverses his transformation by convincing him that Serah's soul still wishes to be with him.
In the Dead Dunes, Lightning finds Fang leads a bandit group known as Monoculus, and joins to help in their quest of locating the holy clavis needed for a ritual only Vanille can perform that is said to save the dead. Lightning uncovers a path to the Temple Ruins underneath the desert where she and Fang learn how Bhunivelze created the gods that formed the world and mankind, and find the clavis. When Fang tries to destroy it, a confused Lightning stops her, and during the ruckus the clavis falls into the Order's hands. Fang explains the Order is using Vanille and the ritual she is to perform will kill her, and Lightning urges Fang to meet her in Luxerion on Nova Chrysalia's final day to convince Vanille not to go through with it.
In the Wildlands Lightning finds an injured white chocobo the local legends know as the Angel of Valhalla said to herald the the end of the world. Lightning nurses him back to health and rides him to Etro's temple from where the Chaos is bleeding into the area. She discovers the origin of the Great Chaos is the seeress Yeul's fragmented soul, and meets her numerous incarnations and Caius who yearns for death but is unable to die.
The Yeuls ask for Lightning to save Caius's soul, but she is unable to, as the Yeuls' wish to be with him has bound him to Chaos permanently. Caius and the Yeuls remain at the temple as Lightning moves on, intending to be destroyed alongside Nova Chrysalia as there is no place for them in the new world. Before Lightning leaves, a Yeul reveals that the Angel of Valhalla is the reborn form of Odin, Lightning's Eidolon from when she was a l'Cie. Though the Great Chaos that destroyed the world balance was revealed to be Yeul's paradoxical existence as multiple souls who all yearn to be with Caius, Lumina implies there is one Yeul who longs for someone other than him.
Elsewhere on the Wildlands, Lightning finds her former ally Sazh Katzroy and his comatose son in an abandoned airship and helps collect Dajh's soul fragments to restore him to life, saving Sazh's soul as well. Mog, the moogle whom Lightning had entrusted as Serah's "good luck charm", has reunited with his moogle friends. He leads the Moogle Village deep in the Jagd Woods. At first Mog fears confronting her, as he feels culpable for Serah's death, but Lightning doesn't blame Mog and asks him to be there on the final day when Serah will be revived.
During her quest Lightning meets an apparition of Serah who promises to be with her soon in the new world, but Lightning feels no warmth toward it, and fears she has lost a part of her humanity. Lumina helps Lightning realize Serah's soul has been stolen from her by Bhunivelze, and suggests the apparition of Serah, Hope, and Lightning herself, are but fakes. Lightning implies she will turn against Bhunivelze if he does not fulfill his part of their deal, and Lumina reminds her that in that case Lightning will have to betray Hope, her one friend in Nova Chrysalia.
Lumina tries to remind her of the true self she keeps denying, and implies she knows where the real Serah is. In the dawn of the eleventh day, Lumina shows Lightning apparitions of her friends, and claims Lightning rejects their help. Lightning meets Yeul inside her heart, who implies Lightning is incomplete and thus unable to save anyone, even Serah, before she can first save herself. Lightning begs Lumina to reveal what she knows, but the latter berates her for not realizing what it is that she is missing.
As the end draws near the souls of the dead that reside in the Chaos talk to Lightning in the form of Cid Raines, asking for her help, as Bhunivelze sees them as impurities that need to be purged. Raines asks Lightning to stop the the Soulsong ritual Vanille is to perform and defy Bhunivelze, as Vanille unknowingly can do what Lightning cannot: she can guide the dead to the new world to be reborn. Lightning learns that Chaos must not be eradicated from the world, because it is the material human hearts are made of, the connective tissue that unites all of mankind, a power that gods cannot see. Upon a person's death their soul will melt into the Chaos to await rebirth, Serah's soul included. Lightning thinks if she were to plunge herself into the Chaos and call out, Serah would respond.
On the final day, the Chaos swallows all but the Luxerion Cathedral. Lightning and Fang team up to save Vanille from the ritual, and Lightning learns the Soulsong is part of the Order's intention to destroy the souls of the dead to free those still living from remembering them so they could live in perpetual bliss in Bhunivelze's new world. After being coaxed into listening to the dead, Vanille learns that, despite their suffering, the souls carry the hope of being reborn. Vanille stops the ritual, and Snow arrives and destroys the clavis with Fang's spear. Together, Fang and Vanille guide the dead to the Ark to be reborn in the new world with their souls acting as the guiding light.
Lightning's purpose as the savior of souls is fulfilled as the bells toll to the end of the world and the final day comes to pass. Bhunivelze appears to her and Lightning learns that centuries ago Hope became a puppet body that Bhunivelze has been using to better understand mankind as part of his scheme to purge it of their emotions and free will for his new world. Now having taken over Hope's body entirely, Bhunivelze admits he can't see human souls and thus doesn't know where Serah's soul is.
Lightning seeks Bhunivelze's true body out in Cosmogenesis, an otherworldly dimension where Bhunivelze is in the process of creating his new world. Bhunivelze explains his plan for Lightning to replace the late Etro as the goddess of death and protect the world balance. She rejects the apotheosis and rebels against Bhunivelze, as she desires a world free of gods where humans can decide their own paths in life.
The powers Bhunivelze had granted to make her the savior make Lightning strong enough to take him on. At first she intends to plunge herself and Bhunivelze to the Chaos to free the souls he had consumed, but the simulacrum of Serah Bhunivelze had created to keep Lightning acquiescent appears to her and implores Lightning to find the real Serah. It is revealed that when Bhunivelze had purged Serah's soul from Lightning before making her the savior, Lightning's denied feelings that had always lain latent within her had been made manifest by the Chaos, creating Lumina, who had become a vessel for Serah's soul. Lightning accepts the part of herself she had wanted to deny and Lumina is reintegrated into Lightning, freeing Serah's soul and restoring Lightning's heart to normal.
As Lightning frees Hope's soul from Bhunivelze, Hope saves her from sacrificing herself by plunging both herself and Bhunivelze into the oblivion. Joined by her former friends and allies when they escape the deity's hold, including Serah and the Eidolons, Lightning frees the souls Bhunivelze consumed and uses their collective power to defeat him. With Bhunivelze turning to crystal, Nova Chrysalia is destroyed and all that is left behind is a dark wasteland.
Caius and the various incarnations of Yeul appear before Lightning and her friends and the Yeuls announce their decision to take over Etro's role as the protectors of the dead and keepers of the balance between the realms of the living and the dead. As the realm begins to collapse, in a final act of redemption, Caius allows the final incarnation of Yeul leave with Noel while he and Yeul's other incarnations are drawn into the new unseen realm.
With the old world no more, Lightning and her friends find a glimmering crystal in a void. The Eidolons and Mog bid their farewells and fade away while Lightning and the souls of humanity leave for the new world. Having begun her life anew, Lightning, no longer dressing like a soldier or a servant of the divine, steps off a train in a countryside on a peaceful journey to reunite with one of her friends.