Gran and Vyrn live on the sleepy, far-flung island of Zinkenstill. Their quiet lives are rocked by the sound of a sudden explosion and the sight of battleship in the sky. They follow a light that falls from the battleship into the forbidden woods, where they encounter a mysterious girl.

Gran dreams of his youth, remembering the words his father left in a letter - "I will be waiting at Estalucia, Island of the Astrals." He awakens to find Lyria at his bedside, happy to see him well after the incident with Pommern and the Hydra. Katalina and Lyria explain to Gran the situation he now finds himself in, and that he must now make the bold action to journey with them.

Gran and his party depart Zinkenstill for their goal, the Island of Astrals. However, Katalina crash lands the small airship on a nearby island, Eingana Island. A man named Rackam happens to witness their totaled aircraft. The townspeople consider Rackam an oddball for the way he's always working on repairing a certain airship that has no chance of ever flying again.

Gran and company are under fire and trapped by Imperial Army General Furias, who intends to recapture Lyria. However, Rackam, the helmsman, gives them a way out. They propose hiring him as a helmsman to get them off the island, but he refuses and tells them he doesn't want to fly unless it's with the Grandcypher, the old airship that has captivated him since he was young.

Thanks to his skill as a helmsman, Rackam navigates the Grandcypher to the mass of dark clouds, where Tiamat is waiting for them. Gran and his comrades must face this great primal beast to save the Port Breeze Archipelago and its guardian deity.

After saving the Port Breeze Archipelago from the threat of Tiamat, Gran and company set off for the Valtz Duchy. Siero introduces them to a Valtz Duchy "special operator," who asks them to search for the missing Archduke Tzaka, the most powerful person in Valtz. They take the job and begin investigating right away, but someone is following them...

Gran and company move on to a secret factory in pursuit of a clue to the missing Archduke Tzaka. Lyria says she hears a voice calling out to her and leads the group to the deepest recesses of the location, where the archduke and an iron giant await.

Gran and company visit another island for supplies, and take on an archaeological exploration job for Siero. The group reaches the ruin's entrance, but a series of events causes them to split up into two groups. Cut off from each other, they move forward in order to meet up again, and encounter the treasure hunters Mary and Karva along the way.

The group makes their way to the Auguste Isles, an island holding an entire ocean. While examining a mysterious substance, Rackam runs into an old friend who leads them to the capital city of Mizarea. There, the group splits up to tend to smaller tasks, while Gran and Lyria venture off to see the sights.

The Auguste Isles are taking fire from the Erste Empire's attack. Gran pursues the abducted Lyria, rushing towards the airship landing site, where the empire's warships have appeared. Meanwhile, Pommern makes off with Lyria, but just then, a primal beast, Leviathan, rises from the sea, along with a gigantic column of water.

Gran and company visit the Lumacie Isles in order to wake up the comatose Lyria. Rosetta leads them to a giant tree nestled deep in a forest. She summons Yggdrasil, the primal beast that protects Lumacie, and explains that with her help Gran can enter Lyria's consciousness.

Lyria returns with Gran and the others to Auguste. They see the city, devastated even more by Leviathan's fury. Eugen is on the verge of giving up when Lyria says, "I want to help Leviathan." At the same time, the skilled knights begin working to protect Auguste.