In the near future, spirits and monsters are in full sight. A boy leads a group of people with special abilities as they plot against a massive organization that takes advantage of a certain incident and eventually know the truth about their world in the process.

Oreki Houtarou is a minimalistic high school boy. One day, he joins the Classic Literature Club at his elder sister's request. There he meets Chitanda Eru, Fukube Satoshi, and Ibara Mayaka. Chitanda is a calm beautiful girl but she turns into an embodiment of curiosity once she says, "I'm curious." Fukube is a smiling boy with a fantastic memory who calls himself a database. Ibara is a short girl and is strict with others and herself. They begin to investigate a case that occurred 45 years ago. Hints of the mystery are buried in an old collection of works of the former members of Classics Club. The collection is titled "Hyouka."

Ashiya has spent the first seven days of high school stuck in the infirmary because of a youkai attaching itself to him. He ends up asking the owner of a small tea room called the "Mononokean" for help. This is a tale involving the very morose owner of Mononokean guiding the youkai that happened to wander into this world go to the next world.