Yuuri Mito, sole heir to the Yachimata Shrine family, possesses deep knowledge of Shinto rituals. His passion for automobile maintenance and design fuels dreams of becoming a mechanic or designer, conflicting with his expected future managing the shrine and creating mild tension with his father, who he reluctantly accepts may inherit the duty from.

One spring break, he investigates a relic near his school connected to his shrine's past. While performing a ritual with friends Ameri Kawai and Sankurou Kaname to relocate the relic's spirits, an accident occurs—Ameri's moped crashes into the relic, shattering its seal. This releases the Tayutai, a supernatural race sealed long ago by the goddess Kikuramikami no Hime. The goddess reincarnates as a young girl whom Yuuri names Mashiro after seeing marshmallows. He takes her to his family's shrine, where she declares herself his wife.

With the seal broken, three powerful Tayutai called the "Three Mightiest" escape, harboring hostility toward humans. Yuuri discovers latent spiritual abilities tied to his lineage—a "Demon-repelling Power" effective against Tayutai. He undergoes intense training under Mashiro to master this power. Alongside Mashiro, his childhood friend Ameri, his stepsister Yumina Takanashi, and martial artist Mifuyu Kisaragi, he confronts the Three Mightiest in nonlinear sequences shaped by his choices. His goal evolves into achieving Mashiro's vision of coexistence between humans and Tayutai.

In later events, including sequels, Yuuri marries Mashiro and becomes a father. Together, they lead freed Tayutai and work towards realizing lasting coexistence, continuing the legacy of his ancestor Kageharu Yachimata, the original sealer of the Tayutai.