After graduating high school, Suzukaze Aoba joins Eagle Jump, the game company that developed Fairies Story, the game she obsessed over as a kid. On her first day as a working member of society, Aoba heads to work swaying in a packed, morning rush hour train. She manages to get to the office building all right but hesitates, wondering if it was really okay for her to take that last step and go inside. That's when a senior member of staff, Toyama Rin, shows up at work and safely leads Aoba inside the offices of Eagle Jump.

In this world, Sensha-do (戦車道), the art of tank-combat, is a traditional Japanese martial art for girls. Miho, a girl who just transferred into the Ōrai Girls' Academy in Ibaraki Prefecture, has been ordered by the academy's student council chairperson to join the school team and compete in the national Sensha-do championships.

Surrounded by a forest and a gated entrance, the Grace Field House is inhabited by orphans happily living together as one big family, looked after by their "Mama," Isabella. Although they are required to take tests daily, the children are free to spend their time as they see fit, usually playing outside, as long as they do not venture too far from the orphanage — a rule they are expected to follow no matter what. However, all good times must come to an end, as every few months, a child is adopted and sent to live with their new family... never to be heard from again.

However, the three oldest siblings have their suspicions about what is actually happening at the orphanage, and they are about to discover the cruel fate that awaits the children living at Grace Field, including the twisted nature of their beloved Mama.

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."