Kannazuki no Miko begins in the town of Mahoroba, where both man and nature move slowly. Two kids from the elite Ototachibana Academy in the village might as well be night and day. Himeko is shy and unassailable, but Chikane is confident and graceful. Despite this, they adore each other, and nothing, no matter how hard they try, can separate them. On the two girls' shared birthday, a terrible voice corrupts one of their friends into assaulting them, and just when things looked hopeless, the two girls' latent lunar and sun priestess powers emerge, expelling the evil. However, that was only the beginning. The two must now defend themselves against the innumerable others who would endanger their lives—including the people themselves.