The story revolves around Mahiro Fuwa, a teenager whose sister 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 rest of the Kusaribe clan who intends to awaken the "Tree of Exodus" whose power can bring ruin to the entire world.Several dialogues and plot elements in Zetsuen no Tempest pay homage to two works of William Shakespeare, Hamlet and The Tempest, which are two stories about retribution, albeit with completely opposing outcomes. During the confrontation between Samon and Mahiro amidst the revival of the Tree of Exodus, Yoshino recalled a flashback in which his girlfriend quoted from Hamlet. He replied that it was too unlucky to quote from, and she replied that the situation between him and Mahiro was similar to The Tempest. This realization allowed him to challenge Samon and turn the tides in his favor.