Sentan Island exists in a state of dreamlike tranquility; a small island, surrounded by the Yuden Sea, cut off from the war between the Northern Government and the Southern Continent Free Zone. Akiyuki Takehara lives on Sentan Island along with his mother Fusa. Despite his mother's strained relationship with his father, Ryuzo, the town doctor, the bond between father and son remains strong. One day the island's tranquility is shattered, when Akiyuki, along with his best friends Haru and Furuichi, are caught up in an explosion on a school bus. The explosion produces a mysterious light which enters Akiyuki's arm. With no time to understand what has happened, Akiyuki is transformed into a creature called Xam'd. Akiyuki rampages through the city, only to be stopped by a mysterious girl who offers him a choice: come with her and live, or stay and turn to stone. Accepting her offer, Akiyuki embarks on a journey of discovery that will take him to new lands, and help him to understand the connection between himself and the lifeform known as Xam'd.