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.

Beginning of the Wings and the Heir of the Gods
Twenty years ago, an assassin named Sagi is framed for the death of the Emperor of the Alfard Empire.

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.

Beginning of the Wings and the Heir of the Gods

 * Sagi works for the Alfard Empire in an elite unit, the Dark Service, that reports directly to a powerful politician, Lord Baelheit. He is joined by Guillo, who, while resembling a mechanized puppet, is actually sentient and animated by magic. The unit is given a dubious assignment to assassinate Emperor Olgan, although the ultimate source of the order is unclear.
 * Before the two have a chance to actually carry out or reflect on the morality of this act, Olgan is killed by a third party.
 * Blamed for the murder, Sagi and Guillo are then forced to flee, with a man named Geldoblame helping them in escaping while suggesting they meet up with his master, Quaestor Verus, due to Sagi and Verus both being summoners. During their escape, they encounter a giant beast called an Umbra, which Guillo has been mysteriously programmed to defeat. While trying to leave the city, they meet up with the third member of the party, a young woman named Milly.
 * The three of them must work to clear Sagi's name while trying to uncover the nature of the threat caused by the maneuvering of Alfard's various power-hungry politicians, as they work under Alfard's Quaestor Verus.
 * The main enemy eventually turns out to be a being named Wiseman, a sorcerer with a thirst to turn every being in the world into pure Magnus.
 * As Sagi, Milly and Guillo go back and forth between the present and a "dream world", they eventually discover the reason why the evil god Malpercio was created.
 * It is revealed that Sagi's spirit connected to that world, and that Sagi is not a spiriter at all, but is instead part of the Empire's malideiter project.
 * Flashback: This came about as a result of experiments which Lord Baelheit was ordered to perform on behalf of Emperor Olgan in an effort to create artificial spiriters, rivaling their power with Malpercio's afterlings. Although the experiments were ultimately abandoned after a mishap, the test subjects were released still containing pieces of Malpercio.
 * Years later, while stopping the maniacal plots of the politicians, Sagi learns of his true nature and must attempt to reach equilibrium with the being inside him or risk certain death.
 * Slightly later, Milly's true intentions are revealed, as well as her past, and connection to Baelheit.
 * Flashback: Milly is half-Machina; when she was just a child, a failed experiment (along the lines of the one which created Sagi's "spirit") tore her in half and killed her mother. With the help of his own guardian spirit, Baelheit managed to revive Milly using Machina.
 * Perhaps one of the greatest obstacles encountered during the quest is the Machina Vanguard, consisting of three high-ranking Mintaken officers, Valara, Heughes and Nasca (who is Heughes' younger brother), who report to Lord Balheit. They hold the power of Machina Armas, the strongest weapons in Machina warfare, and thwart the plans of Sagi and his comrades several times over the course of the adventure. However, after joining powers with the force inside him, Sagi acquires immense strength. With this strength, he is finally able to defeat the Machina Vanguard that were pro-machinating each of the floating continents. He then sets off to defeat Baelheit once and for all.
 * In the interim, though, Baelheit finishes construction on a huge flying fortress built completely out of machina called Tarazed. He orders that everyone move onto the fortress, as he intends to destroy the continents.
 * Verus orders Sagi to stop Baelheit, and although Sagi does so, Verus reveals he has been pulling the strings and using the group for his own ends.
 * The group defeats him, but Wiseman, who had possessed Verus, attacks the group.
 * With the aid of the members of Malpercio, Sagi is able to defeat Wiseman, but this leads to Tarazed's collapse.
 * Sagi, Milly and Guillo flee, aided by previously defeated villains, Nasca, Heughes and Valara.
 * Guillo sacrifices itself to save Sagi.
 * Sagi and Milly return to Alfard, happily reunite with family and friends, and eventually decide to elope and move to Mira.
 * Verus's prior assistant, Geldoblame, having been backstabbed by Verus before his demise, returns to Alfard and becomes the new emperor and instructs people under him to locate the five "End Magnus" and to bring the researcher Georg before him.

Eternal Wings and the Lost Ocean

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

Beginning of the Wings and the Heir of the Gods

 * Based of Baten Kaitos Origins.