After spending a majority of his life in an orphanage, aspiring doctor Uryuu Kamihate has finally found a place willing to take him in—the Amagami Shrine. There is only one problem: he is an ardent atheist.

Arriving at the shrine, Uryuu discovers that he will not be alone. Living with him are three shrine maidens: the childlike eldest sister Yae; the confrontational middle sister Yuna; and the mischievous youngest sister Asahi, all members of the Amagami household. While Yae and Asahi welcome his company, Yuna refuses to accept his presence and repeatedly clashes with him over their contrasting beliefs. However, Asahi soon unravels the reason behind his lack of faith.

Just as things are beginning to settle, Chidori Amagami, grandfather of the three sisters, suddenly reveals the condition for Uryuu's stay: he must marry one of the sisters and inherit the shrine.