The story of Tayutama revolves around the male protagonist Yuuri Mito, a third year high school student who is a descendant of the Mito family of the Yachimata Shrine. One day during spring break, Yuuri and his friends Ameri and Sankurou discover a wooden relic which bears mysterious symbols in the school's woods. The relic turns out to host the Tayutai race which the shrine worships, but is deemed to be insignificant for preservation by the school, and will be demolished to allow the school grounds' expansion. Yuuri later sneaks into the school to transfer the relic's spirits, after coming to the conclusion that destroying the relic may be harmful. As he performs the ritual, he accidentally summons Kikuramikami no Hime, a Tayutai goddess who explains the belligerent relationship between humans and Tayutai, and materializes as a young girl, hoping to maintain a mutual relationship with humans. The relic is then destroyed after an accident caused by Ameri, which accidentally releases the entire Tayutai race, among whom are Nue and Oryu, two other influential Tayutai who hold humans in low regard.