Thousands of years ago, a man called Feolthanos was the chief of the Aegyl when they still lived in Ivalice. Feolthanos took a Viera wife and started a family; their descendants eventually being called "Feol Viera." He revolted against the Occuria and took the Aegyl to Lemurés, using the Auraliths to create a barrier around Lemurés and to keep the Occuria out while trapping the Aegyl there. It was maintained until about a year ago when a massive amount of Mist from the Sun-Cryst was released upon Ivalice.
Feolthanos left the Cache of Glabados and along with a book as a gift for his family (who didn't have wings), in the hopes that one day they would use them to come to him in Lemurés. The Cache is actually three shards of Auracite which each serve as a beacon to call the Galbana, an airship built by Feolthanos that picks up the one who finds the Cache and bring them to Lemurés.
Feolthanos' plan was foiled by Vaan and his friends, who instead took command of the Galbana and used it to explore Lemurés, where Llyud told them of the mass of sky pirates invading the Purvama in search of treasure. At the site of beautiful auralith at the Fane of Tehp Qul, Vaan's party came face to face with the Judge of Wings, a person completely clad in armor who sought to destroy the auraliths. Though the Judge was temporarily defeated, she managed to shatter the great skystone and abscond with its power.
After fruitless leads from the Sky Pirate Rikken, Tomaj located the Judge at the Yapih Caverns, who had begun a ritual at the caves' fiery skystone. Vaan's party escaped the clutches of Ba'Gamnan and confronted the Judge, only to flee when she summoned Bahamut, who broke the Muruc Cahuac Skysea into pieces.
Bahamut's wrath sent the Galbana into a crash-landing at Tswarra, Isle of the Lost, where the protagonists found a wounded man by the name of Velis. After nursing him back to health, Penelo was able to discover Velis' true nature as the dead love of Mydia, the Feol Viera behind the Judge of Wings' faceless helm. The Judge herself appeared on the deserted island, changed Velis into a terrible Yarhi, and ordered him to attack Vaan's party. Though Penelo refused to hurt her friend, the rest of the crew fought, and though the Judge escaped again, Llyud dealt the finishing blow to Velis, ending his warped life.
The Galbana repaired, Vaan and company met up with Fran at Arda, Heaven's Pillar, after rescuing her from the tireless Ba'Gamnan. The Viera led them to the Ymir Qul Underground, where Balthier and the Judge of Wings waited next to the second auralith. The Judge and her cohort, Mateus, were defeated and left the area, but Balthier intended to carry out his plan for the destruction of the auralith. Despite Vaan's efforts, Balthier and Fran succeeded, and the release of energy from the skystone sent Vaan, Penelo, Llyud, Filo, and Kytes to Lesrekta, Isle of Illusions.
Lesrekta served as a test for Vaan's true feelings towards his friends. After being separated from one another throughout the misty island, the five reunited after Penelo expressed his wishes for Vaan to come back. They were called by a voice to Illusion's Home, where the spirit of Velis lingered. He begged them to send him on properly, and explained Mydia's true existence as a puppet of Feolthanos. After his defeat, he begged Vaan to save Mydia from Feolthanos' clutches and turned himself into the godblade Anastasia. Velis' passing also prompted Vaan and his friends' return to the real world, upon the Galbana.
After Balthier explained that he destroyed the auralith to protect the aegyl souls within from Feolthanos, he and Fran joined the party, which promptly met up with Queen Ashe and Basch on the Dreadnought Leviathan. Descending to Ivalice, Vaan and company followed several leads on the Judge until they met her at the Feol Warren, the secluded home of the Feol Viera. Mydia had killed the penultimate members of her own race, with the intent to give them, in death, escape from Feolthanos' will. Vaan's party defeated Mydia for the final time, and as she died, she told them of her loss of Velis and the attempt to bring him back to life, which led only to the giving of herself to Feolthanos in the false hope he would resurrect her fallen love.
Mydia's spirit led the Galbana to Eternity's March, the gateway to the Feolthanos' fortress, the Keep of Forgotten Time. Here, the party learned the history of the aegyl and their unending struggle against the Yarhi, who were created from their ancestors' departed souls in order to fuel Feolthanos' need for anima. The aegyl god served as the final auralith, a leech that drained the souls of his people and continued the perpetual cycle of aegyl's suffering. Feolthanos had been forced to commit this act by the Occuria, in vengeance for leading his people to the skies of Lemurés.
After Feolthanos' defeat, he was freed of his eternal bonds and died, and the auraliths' power died with him. The Purvama of Lemurés, no longer supported by the anima of its countless aegyl inhabitants, fell from the sky, and Llyud bid farewell to his friends in order to lead his race to a new home. The Galbana flew off of its own accord above the disintegrating islands of Lemurés, as its former commanders returned to Ivalice aboard the Strahl.
At the end of the game, if everything is completed, a secret cutscene is shown where Vaan and Penelo try to sneak away from Rabanastre, only to be found out by Filo and Kytes; being none to happy about being ditched, they proceed to summon Yarhi to chase the duo into the night, with Vaan carrying Penelo. Penelo also kisses Vaan during the cutscene.