After witnessing his mother's death at a young age, Uryuu Kamihate grew up disillusioned with the gods, dismissing faith in them as utter nonsense. Due to his beliefs, he aims to become a doctor, spending most of his time studying to enter the prestigious Kyoto University.

To further his studies, Uryuu searches for a new place to take him in and get away from the noisy environment of the orphanage where he grew up. Chidori Amagami, head priest of the Amagami Shrine, allows him to stay at the Amagami residence. However, Uryuu has to live there with Chidori's three granddaughters—Yae, Yuna, and Asahi—who serve as shrine maidens. Moreover, Chidori has another condition for Uryuu: he has to marry one of the sisters to ensure the shrine's future and one day inherit it. But with Uryuu's goals and outlook naturally clashing against the sisters' beliefs, this already daunting ordeal seems outright impossible.