From Penelo’s diary: It was over before it started. We’d only just began to spread our wings, and they were taken away. Vaan shrugged it off. He said he’d buy a new airship, and he never even talked about the treasure he’d found. It was as though our adventures were only dreams, dreams that faded day by day under brilliant Rabanastre skies. We went back to the quiet lives we’d always led, like nothing had ever happened. But it wasn’t to last...
Vaan is the last one to arrive at the Glabados Ruins. Penelo, Balthier and Fran are already inside, waiting for him. Their intention is to take the treasure within. The Esper Ifrit is guarding the treasure, which the team find out is a pair of stones. Balthier and Vaan take one stone each and run away as the ancient building comes falling down.
After this adventure, Vaan and Penelo return to their quiet normal lives in Rabanastre, or so they thought. Whilst dreaming about adventures to come, Vaan and his friends find out that an ancient derelict airship is headed their way. That night, Vaan goes with his friends Filo and and Kytes to take a closer look at the mysterious vessel without telling the overprotective Penelo. He then tells his astonished friends that he wants to claim the airship for himself since it was abandoned anyway before being recently found. Once aboard, Vaan discovers that his stone is magically interacting with a floor panel adorned with strange symbols, and soon learns that he can use it as a gate to summon Espers that obey their every command. A group of headhunter lizards, led by Ba’Gamnan, have the same idea to steal the airship, and so a fight ensues. As the last lizard drops to the floor and gets fettered, the airship starts moving, just in time for Penelo and Tomaj to join their friends.
Arriving to their destination on auto-pilot, Vaan and his companions realise that they have made the trip to the legendary sky continent. As per the sky pirate code, the first thing to do is to name the airship, which they name the Galbana. Upon landing, Vaan, Penelo, Kytes and Filo go out to explore the land, whilst Tomaj stays behind to keep a watchful eye on Ba’Gamman. While exploring the verdant woods of the Bosco Pampa, and picking up treasure along the way, they see a man being attacked by antlions and decide to help him. Once he gets up on his feet, the winged man introduces himself as Llyud. He is also an aegyl, the local winged race of the sky continent of Lemurés.
Llyud tells the newcomers that the sky continent was protected by a barrier, hidden away from the other races that dwelt on the land below. However, some time ago a rush of Mist has breached the barrier, and sky pirates have begun to plunder Lemurés. This caused the Espers, which are also called Yarhi by the aegyl, to start attacking people. Vaan and Penelo suspect that the rush of Mist was caused by the explosion of the Suncryst which they were involved in about a year before. Maybe to make amends, they tell Llyud that although they are sky pirates themselves, they will help him get rid of the other intruders. Llyud also reveals that the Yarhi are summoned from the realm of illusion by means of the auracite, and were created by the aegyl’s god who is called the Eternal. It so happens that the stone that Vaan is holding is a piece of auracite.
Whilst looking for sky pirates in a temple, Vaan and his party end up in a chamber where a huge Titan attacks them. Seeing his friends trapped inside, Tomaj sends Ba’Gamman, who is forced to cooperate by means of a torture device, to help them and get out with Titan joining their ranks as an Esper too. Deeper in the temple, our heroes find out that the other sky pirates are trying to gather auracite and auraliths, but they are simply mercenaries hired by the mastermind who is just referred to as the Judge of Wings due to her appearance. Llyud adds that Feolthanos, the Eternal, had created the sky continent and added three auraliths whose purpose was to create the barrier. Their destruction would put Lemurés in peril.
Llyud knows the location of one auralith, which is enough for the team to decide where to go next. At the Isle of the Megalith in the Kisne Rise, they find that sky pirates are already attacking the temple of the auralith, and Vaan orders his own group to join the aegyls’ side to repel the attack. To enter the temple itself is another matter altogether as it is heavily guarded. Vaan decides to sneak in and open a secret passage for the others to get in too. Inside the temple there are four more pirates. These ones however, are trying to destroy the auralith crystal. As soon as Vaan and his friends stop them, the Judge of Wings walks in. At first she tries to offer them a job just as she did with all the other pirates, but seeing her offer refused she summons the ice Esper Shiva to keep them busy while she breaks the crystal.
On their way back to the Galbana, the good space pirates are ambushed by Ba’Gamman’s brothers. The lizards’ purpose is to stop them from following the Judge of Wings, but instead end up telling Vaan that the Judge is headed for the skysea. There, the infamous pirate Rikken and his sidekicks Elza and Raz are organizing an auracite gathering tournament. The entry fee of one hundred thousand gil is too much to ask the other pirates though, not to mention that it also sounds suspiciously like a scam. Filo manages to get Rikken to accept to waive the entry fee, but at this point Rikken decides to also join the competition for the treasure hunt.
At first, Vaan plays along with Rikken after that Rikken boasts that he knows everything about the Judge of Wings. It turns out that Rikken is of no help at all, but fortunately Tomaj manages to find some information about an underground temple deep inside the Yapih caverns. There, Filo is captured by Ba’Gamman, but with Rikken’s help Vaan manages to free her. Soon after, everyone’s feelings start going haywire, meaning that the Judge of Wings is not too far, although Llyud feels nothing of the sort. Wanting to get rid of her followers, the judge summons the giant Belias and other minor Espers, which Vaan and his companions are quick to defeat. Seeing this, she finally summons Bahamut.
The next thing they know, the Galbana’s crew end up marooned in an unknown place with their vessel in need of repairs after that the skysea has been blown up. Here, Vaan and his friends save a man from being attacked from the local Yahri. The man does not utter a single word to them though. However, he establishes a special connection with Penelo after that she dances to cheer him up. Vaan is visibly envious of this man who later introduces himself as Velis.
Kytes and Vaan go around to hunt for food, whilst Penelo and Velis start feeling really close to each other. Velis confides to his new friend that he is looking for Mydia who is the woman he loves. Vaan of course is jealous that Penelo is spending so much time to get to know the newcomer. One night, Velis takes Penelo out for a walk, and reveals to her that in reality he is dead. Whilst Penelo talks about this to her companions around the fire, the Judge of Wings appears to tell them that she is Mydia before Velis disappears into thin air. It is at this time that the sky pirates find out that the aegyl do not have any emotions since they have lost their anima.
The airship is fixed! Llyud, hoping to feel some emotions too, asks Penelo to dance for him. Somehow, everyone within Vaan’s party now feels closer together. They manage to forge pacts with some powerful Espers before heading towards Heaven’s Vigil. Here Ba’ Gamman uses his henchmen and other mercenaries to try to capture Fran in order to lure Balthier to save her, but as usual Vaan comes to help. She decides to join the party and leads them to her partner.
In a cavern upon the sacred mountain, Vaan and his companions witness a fight between Balthier and Mydia, with an auralith in the background. They help him out, hoping that by defeating the Judge of Wings they will save the stone. However, Balthier is of a different opinion, and once he is saved, he proceeds to destroy the auralith. Balthier tells Vaan that there are things that Vaan still cannot comprehend and that the stone must be destroyed for his own good.
After the auralith explodes, Vaan and his friends end up on Lesretka, Isle of Illusions. At first Filo thinks that they are dead and find themselves in some kind of afterlife. In reality, Vaan cannot see his companions and goes through the woods to look for them. Llyud tells Penelo that they have gone through the other side of the portal when the auralith was destroyed, and so they are now located in the land of the Yarhi. Through their will to find each other, Vaan and his party are rejoined again. Now they have to find a way to go back to their world.
Velis reappears in the world of illusion to meet Penelo again. He explains that he wished them to come here because Feolthanos was using the auraliths to steal the anima of the aegyl to turn them into Yarhi and he must be stopped. Llyud begins to understand why he has no emotions. Velis adds that his very self was created by Mydia’s imagination and now he lives here as a Yarhi. Against Penelo’s wish, he now wants them to kill him so that Mydia can get back some of her anima that she lost when creating him. Finally he adds that Feolthanos is gathering his power from the auraliths and he will soon invade Ivalice, so the auraliths need to be destroyed. Vaan now starts to comprehend Balthier’s actions.
After that Velis is finally laid to rest, Vaan and his friends find themselves back on the Galbana. They find out that Balthier’s airship, the Strahl, is in need of repairs and while they were away in the land of illusions its crew members have come upon the Galbana. After a heated discussion between Vaan and Balthier about the latter being a manipulator, Balthier and Fran join Vaan’s party. No time to dwell on the hospitality however, the ship is under attack by the aegyl, who now seem to have their animas back! It is time to fend them off.
The history of Lemurés starts to unfold itself. Thousands of years ago, a godlike race known as the Occuria started to dominate the other races in Ivalice. The aegyl fled to the skies in order to escape from their grip. They constructed the auraliths to erect a barrier that would keep them hidden from everyone else, but it was to be the start of their doom. The only way to save the aegyl now is to find Feolthanos, defeat him and destroy the last auralith. Problem is, only Mydia knows where he is hiding.
After the aegyl, the Galbana gets another group of visitors. This time it is Queen Ashe that comes to seek the assistance of Vaan’s growing party. Basch, her assistant, pleads with Vaan to intervene quickly as other sky pirates are wreaking havoc by unleashing Yarhi upon Ivalice. Vaan and Penelo accept and together with the Queen they proceed quickly to approach stable land once again, heading towards the outskirts of the city of Dalmasca. As they suspected, they find out that the havoc is being caused by the Judge of Wings.
The answer may lie in the Glabados Ruins, where they find ancient writing from Feolthanos that describes how this place is a gift for his viera wife and children. The very treasure that Balthier and Vaan had found was a trigger to call the airship of Feolthanos which was supposed to bring his family back to him. Vaan and the rest of the crew were riding on a ship that belonged to the Eternal! Near Rabanastre, they manage to get some more information about Mydia and her location. Mydia seems to be of a particular fair-skinned viera tribe who have short ears and are called the Exiled, descendants of Feolthanos and his viera wife. The only way to find out more is to head to the north, to a place called the Paramina Rift.
Apart from freezing temperatures, Vaan and his party find a memorial that was erected to commemorate the fallen soldiers of the battle of Nalbina. Filo spots the name of Velis among those of the other soldiers, just as Mydia shows up and confronts Basch, who repels her attack with the aid of his companions. Back on the ship, Filo and Kytes show the others a map that they had found in the ruins. The map contains the location of the hidden village of the daughters of Feolthanos, precisely within the volcano in Bervenia. The Galbana travels there so its passengers can stop whatever the Judge of Wings is doing. Surprisingly, she lets them defeat her.
Before leaving the mortal world, Mydia says that she left her home and her mother when she was young. She felt alone until she met Velis, but then he left for the war and never came back. Then Mydia sought the help of her patriarch, who forced her to do his bidding. Facing Fran, she asks them to seek and destroy Feolthanos, thus ending his suffering that is caused by his eternal curse. On their way to the Eternal, Vaan and his party still have the time to have a fighting contest with Rikken and give another lesson to Ba’Gamman. The end of the world can wait!
The Galbana proceeds to the Keep of Forgotten Time in order to fulfill Mydia’s dying wish. Here, its crew are greeted by the illusions that the Eternal concocts. Wave after wave of aegyl come to attack them, and wave after wave of aegyl fall down. They continue fighting through the horror that lurks in this place. Feolthanos justifies his actions saying that he stole the anima of his fellow aegyl so that they do not feel any more suffering. And now he steals Llyud’s anima.
After going through the illusions, Vaan and his party come face to face with Feolthanos. Before them they see a being who has preyed so much upon the anima of his followers that he has become a crystal too. He tells his visitors that he had to do what he did because he was seeking revenge against the Occuria. In a flash of light, Feolthanos turns into a huge winged monster and is now waiting for his visitors inside the inner chamber. After a tearful speech, Vaan sends his comrades to charge the attack against the Eternal.
Feolthanos is no push over. He repeatedly summons more waves of Yarhi to fend off his attackers, but he does have some weak spots. Vaan and his friends press on the attack, until the Eternal starts cracking. Vaan is in a quiet place now. Feolthanos, sitting on his throne, interrupts the silence by calling Vaan for a duel. After some time clashing swords, Vaan thinks that he is done for as his winged opponent seems to have the upper hand.
Suddenly, Filo and Kytes come to Vaan’s support, the first one throwing a fireball towards the Eternal. Llyud soon follows suit and attacks. Feolthanos still stands defiantly before them, but one by one all of Vaan’s friends come to lend a hand in the ultimate battle. The last one to step in is Penelo, who casts a healing spell on Vaan, who in turn is prepared to give his opponent the final blow. With his dying breath, Feolthanos asks Llyud to guide the aegyl to their glory and thanks everyone for bringing peace to the world before flying off.
By defeating the Eternal, the anima are released and the aegyl can be their whole selves again. As Llyud bids farewell to his friends, Lemurés starts crumbling down below. Yet, the aegyl are now free to shape their future however they wish. “The future can be a scary thing. Uncertainty always scares us. But we know that as long as there’s a sky above our heads, there’s hope. Whatever the future brings, all we really need is someone to face it with — together.”, Ship’s Log, Final Entry — Penelo