The peaceful Sentan Island is suddenly drawn into a violent war when a mysterious white-haired girl launches a terrorist attack. But one of the survivors of the attack discovers he has been infected with the Hiruko, a powerful spirit that transforms him into the mecha/human hybrid known as Xam’d.

A headstrong air kayak pilot named Nakiami takes Akiyuki with her onto the giant airship Zanbani. There, she begins to help him learn to control the awesome power of the Xam’d within. But not everyone on this flying ship is happy the dangerous young man is on board.

Nakiami uses a strangely powerful needle to help Akiyuki control the Xam’d. But the spike is not strong enough to conceal the spirit. Sensing the presence of the Xam’d on board the Zanbani, humanforms begin to attack the ship and Akiyuki begins to realize just how dangerous the spirit within him actually is.

To help Akiyuki gain clues about the Xam’d inside him, Nakiami takes him deep into the belly of the floating airship. There, he meets the mysterious seer, Madam Tenshin who advises him to discover what the Xam’d is seeking. Meanwhile, the Free Zone military unit begins construction of an anti-humanform base on the once-peaceful Sentan Island.

When she sees a black market pirate ship, Nakiami disobeys her captain’s orders to meet with Zeygend, the captain of the pirate ship. On Sentan Island, the Free Zone military begins using innocent Islanders in their humanform experiments. Unaware of these secret tests, Haru and Furuichi believe joining the military is the best way to do their part in ending the war.

Haru and Furuichi join the Free Zone military. And Furuichi discovers he has an amazing gift for learning to operate the powerful Mainsoul mecha used in battling the humanforms. Meanwhile, Captain Ishu and Nakiami clash over their opposing views of the humanforms when Nakiami disobeys orders to help a humanform from turning into stone.