Energy-conservative high school student Houtarou Oreki ends up with more than he bargained for when he signs up for the Classics Club at his sister's behest—especially when he realizes how deep-rooted the club's history really is. Begrudgingly, Oreki is dragged into an investigation concerning the 45-year-old mystery that surrounds the club room. Accompanied by his fellow club members, the knowledgeable Satoshi Fukube, the stern but benign Mayaka Ibara, and the ever-curious Eru Chitanda, Oreki must combat deadlines and lack of information with resourcefulness and hidden talent, in order to not only find the truth buried beneath the dust of works created years before them, but of other small side cases as well.

On Christmas Eve, a TV broadcasting station receives a phone call. The caller warns "I have set up a bomb at Ebisu in Tokyo." A contract worker for the TV broadcasting station and a housewife are accused by the Ebisu police as being the culprits. During this chaotic situation, a mysterious man silently watches as everything unfolds. A video clip is then uploaded to an online video website. The video contains a demand to talk with the Prime Minister during a live broadcast or a bomb will be detonated at 6 pm in Shibuya, Tokyo. Who is behind the bombings and who will stop them?