Kanokon's story revolves around Kouta Oyamada, a young first-year high school student who moves from the country to the city and thus transfers to Kunpō High School. On his first day at his new school, a beautiful second-year female student named Chizuru Minamoto asks him to meet her alone in the music room. When he arrives, she reveals her that she is in fact a fox deity and from that day on the two hang out together.