Oreki Houtarou is an "energy-saver" kind of guy, who expends as little energy as possible to do only things he has to. When he starts high school, his older sister sends him a letter asking him to join the Classics Club. The club meant a lot to her, and its number of members has been reduced to zero.

Houtarou reluctantly signs up for the club, only to find that someone else has joined, too! She's Chitanda Eru, a cute, big-eyed girl with an overwhelming sense of curiosity. A mystery crops up that catches Eru's interest, and also draws in Houtarou's friend, Fukube Satoshi. They continue solving mundane mysteries together, and soon they draw in Satoshi and Houtarou's friend, Ibara Mayaka, as well. Mayaka has had a blatant crush on Satoshi since middle school, but he always fends off her advances. Together, they search for the truth in a mystery that involves the history of the Classics Club.