The God of Thunder has been slayed. Adversities of the war have caused the ley line contamination, and the head shrine maiden kitsune Saiguu sends her apprentice, Yae Miko, to perform a cleansing ritual to protect Sacred Sakura roots all over Inazuma. On Kannazuka Island Miko encounters her old friend Urakusai, who manages to foist two human twins, Makoto and Ei, onto her. The three of them embark on the cleansing pilgrimage, unveiling the truth about the slain God and the fate of Inazuma.