The story revolves around Mahiro Fuwa, a teenager whose family was mysteriously murdered one year before, and his friend Yoshino Takigawa. Mahiro is contacted by Hakaze Kusaribe, the leader of the Kusaribe clan who was left stranded on an unknown deserted island by her followers, and agrees to help Hakaze in exchange for her help to find out the culprit for the death of his family. Upon learning of his friend's intentions, Yoshino joins him on his quest to stand against the Kusaribe clan who intends to awaken the "Tree of Zetsuen" whose power can bring ruin to the entire world.