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.

Nakiami performs a special treatment to contain the power of Xam'd in Akiyuki's right arm. At the same time his family and friends look for his whereabouts.

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

Nakiami meets some old acquaintances of hers, and the rest of the crew wonders if she will leave the ship to join them. Meanwhile, a classmate of Haru and Furuichi who lost her entire family surrenders herself to despair.

Haru finally got news from Akiyuki, but just after she and Furuichi joined the military, they are assigned to engage a rogue Xam'd who broke out from a research lab.

Akiyuki receives Haru's letters and after learning that she will be waiting for him at Tsumebara Pass, he leaves with Roppa to meet her. However, he encounters more people turning into humanforms along the way.

Akiyuki and Haru meet again in at Tsumebara Pass, but their reunion is cut short by an angry Furuichi who confronts him after discovering that he became a Xam'd.

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.

Raigyo asks for the crew to take a picture together while Haru decides to follow with her military career.

The crew of the Zanbani must fend off an assault by Humanforms from the Northern forces.

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.

Akiyuki notifies Haru about his return to Sentan Island but in doing so alerts the military to his presence as well. After a brief visit with his father, Akiyuki meets Haru only to have their reunion crashed by a Furuichi who is eager to use his new found power.

Furuichi loses control of his powers and goes berserk, but after being defeated by Akiyuki, he returns to normal. The army intervenes and arrest Haru and Furuichi, while Akiyuki gives cover for Nakiami to escape by holding Commander Kakisu hostage.

Akiyuki loses his sense of self, and with his Xam'd mask permanently affixed, he is captured by a slave trader. Meanwhile, Nakiami continues her journey and meets Yango, a young boy who also became a Xam'd.

Nakiami and Yango continue their journey while the southern army starts to perform experiments on Haru's younger sister, and a mysterious creature persuades a kind old woman to buy Akiyuki from the slave traders.

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.

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

Ryuuzou and Haru's father set off to rescue Midori from the East Autonomy Military Facility. Akiyuki and Haru venture further into the Quickening Chamber.

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.

The Hiruken Emperor is free. Haru, Nakiami and Akiyuki encounter Midori transformed and join forces to stop her.

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.