Baten Kaitos (Nintendo Cinematic Universe)

Baten Kaitos is a Japanese graphic novel series.

Eternal Wings and the Lost Ocean
Guided by a mysterious guardian spirit, Kalas goes on a quest to take down the Alfard Empire who murdered his family.

Eternal Wings and the Lost Ocean

 * Kalas, in his travels to avenge the death of his grandfather and brother, joins Xelha, a good-willed but naïve traveler. Together, they inadvertently release the first of the "End Magnus", which is quickly seized by members of the Alfard Empire, a hostile nation on one of the islands.
 * The two chase after them to the Empire's capital, stopping at Diadem along the way, where they meet and team up with Gibari, a fisherman, and Lyude, Diadem's ambassador to the Empire. Upon arrival, they learn there are five End Magnus in total, and the Empire wishes to locate all five of them, which together, will unseal the power of the evil god Malpercio.
 * The party begins an unsuccessful effort to obtain the End Magus to keep them away from the Empire. One is found in Diadem, but is stolen from them immediately. They travel to Anuenue, where they team up with Savyna, an ex-mercenary from the Empire, but are stopped from obtaining an End Magnus by the Empire's emperor, Geldoblame.
 * They travel to Mira, Kalas's home nation, where they meet Mizuti, a strange masked being who joins the group. A temporary arrest for being suspected of kidnapping Miran resident Lady Melodia causes them again to lose the only End Magnus they had obtained there.
 * The group escapes to Alfard to stop Geldoblame, but in the confrontation, it is revealed that Kalas had secretly been working for Melodia all along to find the End Magnus and revive Malpercio for her benefit.
 * Melodia takes control of the Empire from Geldoblame, and his former soldiers drive him to the depths of Alfard's Lava Caves.
 * Kalas absorbs the power of the five End Magnus and falls under Malpercio's control.
 * The other members are captured and imprisoned, though Xelha escapes and frees them. They travel to Wazn, an island covered in snow, where they learn that Xelha is its queen. She obtains the Ocean Mirror, a special item that allows Xelha to restore Kalas's free will.
 * Malpercio and Melodia refuge themselves into Cor Hydrae, an ancient fortress also unsealed by the five End Magnus.
 * Kalas, feeling guilt over his deception, vows to re-seal Malpercio.
 * Mizuti directs the group to her homeland, a village in the lands below the Taintclouds, a poisonous layer of gas below the floating islands. They venture down to seek the power of the "Sword of the Heavens" to aid their quest; however, Malpercio and Melodia show up, and the two sides clash.
 * The party is able to ward them off, but the Sword of Heavens is broken in the process. The party then learns of one last hope of stopping Melodia and Malpercio: the Magnus of Life.
 * Flashback: Kalas's scientist grandfather, Georg, under the direction of Emperor Geldoblame, used this power to artificially create life - namely Kalas and his brother, Fee. Geldoblame felt Kalas was too human, and only had one wing, and ordered his death. Georg instead fakes his death by blowing up his laboratory, and secretly flees to Mira with Kalas and Fee. Because he was created by the Magnus of Life, however, Kalas can use its power, though he does not yet know how to tap into it.
 * The party breaks through into Cor Hydrae for a final showdown with Malpercio and Melodia.
 * Malpercio is defeated, Melodia receives free will again, and Kalas, Melodia, and the Guardian Spirit use their powers to release Malpercio's spirit from his body.
 * The energy needed to break the shield around Cor Hydrae drains the energy that allows the five major floating islands to float in the sky, and the islands fall toward the Earth below.
 * However, the planet has now become inhabitable again, and with the help of the five ancient gods, the islands safely fall into place on the planet as continents.
 * While the general population celebrates a bright new future, Xelha privately confides to Kalas that she is an ancient ice queen, and that her death is required in order to restore the oceans of water necessary for humanity to exist again on the planet.
 * A final battle with Geldoblame ensues, and Kalas and Xelha defeat him, but the battle uses the last of Xelha's strength and she dies in Kalas's arms just after confessing her love.
 * All over the world, a rain begins to fall, accumulating into the long-lost ocean.
 * With resolution found, it is deemed time for the "guardian spirit" to leave, with Kalas and the others congregating to say their goodbyes.
 * The guardian spirit sticks around just long enough to see an area boy give Kalas a pendant Xelha had worn throughout the game, saying that he can hear Xelha's voice in it; Kalas puts it up to his ear, and Xelha reappears in a flash of water.

Eternal Wings and the Lost Ocean

 * Based on Baten Kaitos: Eternal Wings and the Lost Ocean.