Red Data Girl tells the story of 15-year old Izumiko Suzuhara, a girl who was raised at the Tamakura shrine, a shrine that is part of the Kumano Shrines World Heritage Site. Izumiko has the ability to destroy any electrical device she touches. She is a shy teen-ager with a dream to live in the city so her guardian Yukimasa Sagara suggests that she enrols at Hojo High School in Tokyo where his son Miyuki is also a student. One day while Izumiko is on a middle school field trip, a deity named Himegami appears to her. She learns that she is a yorishiro, a vessel for a kami. She also finds out that because of that Miyuki has been tasked with protecting her.