Tokyo Butei High School is a special school where armed detectives—"Butei"—are trained to use weapons. Kinji Tōyama is a second year student who has a special ability, but he keeps it a secret to maintain an ordinary, peaceful life. However, when he gets caught in a bombing on the way to school, he encounters Aria H. Kanzaki, the most powerful S-Rank Butei student in Assault Studies.
Hotaro Oreki doesn't like to do things that he considers a waste of energy. However, things start to change when he enters high school because even though he does not want to join any non-compulsory school activities, his older sister requested that he join the memberless Classic Literature Club so that it won't get abolished. Unbeknownst to him, another student, Eru Chitanda, already planned to join; but instead of being free from club obligations, Hotaro eventually joined as he is strangely unable to refuse or escape from Eru's passionate gaze of curiosity. Together with his friends Satoshi and Mayaka, they began to discuss a variety of mysteries in school that only H?tar? seems to be able to solve, including the mystery that lingered on from Eru's childhood memory.