Uryuu Kamihate, a young man raised in an orphanage, lands a spot at the Amagami Shrine, despite his staunch atheism. In this new home, he joins three shrine maidens: the mature Yae, the fiery Yuna, and the playful Asahi. While Yae and Asahi embrace him, Yuna vehemently opposes his presence due to their conflicting beliefs. Asahi, however, delves into the reasons behind Uryuu's disbelief. Just as tensions ease, a bombshell drops: to remain at the shrine, Uryuu must wed one of the sisters and take over the sacred place.