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.

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.

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

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.

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.

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.

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.