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.

While becoming accustomed to his new environment, Akiyuki begins the distinctive training in order to control his powers.

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.

After the incident at the Zanbani, Nakiami decides to return to her homeland and Akiyuki asks to go with her. Meanwhile, Haru pays a visit to Furuichi and finds that he too, became a Xam'd.

After fleeing from the military, Haru embarks on a journey to find Akiyuki by herself. Meanwhile, Nakiami learns about Kujireka's dubious plan to wage war against the northern government.

Kujireka asks for Nakiami's support, but is utterly rejected and Haru finally manages to reach Akiyuki and help him to recover his memory.

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.

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.