Zetsuen no Tempest opens with Yoshino Takigawa, an ordinary teenager who is secretly dating Aika Fuwa, the younger sister of his best friend Mahiro. When Aika dies under mysterious circumstances, Mahiro disappears and becomes obsessed with finding the person responsible and making them pay for murdering his beloved sister. Yoshino tries to keep living as usual, but after a month without hearing from Mahiro, he is confronted by a strange girl who holds him at gunpoint—only for Mahiro to arrive in the nick of time and save him.
That encounter pulls Yoshino into Mahiro's search and drags him into a conflict far bigger than a private vendetta. Their path leads them to Hakaze Kusaribe, a witch whose own clan has banished her to a deserted island after internal infighting. Hakaze explains that her brother, Samon, wants to exploit the power of the Tree of Exodus despite her opposition and the danger it poses to the world. Bound together by grief, suspicion, and a growing sense of urgency, Yoshino and Mahiro team up with Hakaze to uncover the truth behind Aika's death while racing to stop a catastrophe that threatens everything around them.