Akiyuki was living a peaceful life along with his friends and family on Sentan Island. This peace was disrupted when sudden war broke out and a strange force took control of his body.

Transformed into Xam'd, Akiyuki confronts the enemy invasion in order to protect his friend Haru. Afterwards he is retrieved by the mysterious Nakiami and taken to the postal airship Zanbani, where she lives.

Raigyo, a Xam'd like Akiyuki, returns to the Zanbani after two years of absence. All members of the crew seem to be happy to meet him again, but Akiyuki somehow does not share the same feeling.

Haru is given a chance to escape confinement while Nakiami finally arrives at her home village, just to be welcomed by the new chief, her younger sister Kujireka.

Nakiami and Yango leave the Tessik village only to see it attacked by a fleet of airships. Akiyuki and Haru meanwhile search for the entrance to the Quickening Chamber

Raigyo and Ishuu continue their assault on the tower. Ryuuzou confronts Commander Kakisu. Akiyuki and Haru learn the truth about the Quickening.

Raigyo and Ishuu make their final push into the chamber of the Hiruken Emperor. Nakiami and Yango leave the Tessik airship to stop the battle over the Quickening Chamber.

Akiyuki confronts the Hiruken Emperor by himself while Nakiami completes her training with Lady Sannova.

Nakiami seals herself in the Quickening Chamber and the confrontation with the Hiruken Emperor draws to a close. However, Akiyuki turns himself into stone, and nine years later, he awakens and reunite with his loved ones.