When Keiichi Maebara moved to the small village of Hinamizawa, he did not expect to make friends so quickly. Now Keiichi's days are spent having fun and playing games with his new companions, and his life couldn't be better. However, one day he sees one of his friends, the tomboyish Mion Sonozaki, working at a maid café. Deciding to tease her about it, his initial joking quickly turns to shock as the girl reveals that she is actually Mion's twin sister, Shion.

As luck would have it, both girls want to spend the annual Cotton Drifting Festival by Keiichi's side. But when Shion breaks the town's sacred rules and sneaks into a sealed shrine during the festival, dragging Keiichi along with her, things take a turn for the worse. Now, Keiichi and Shion find themselves in fear of being spirited away due to their mistake and must find a way to atone before it is too late.