In North Kamakura, tucked away in a quiet alley near the station, stands Biblia Koshodou, an antiquarian bookshop known for its specialty in solving troubles related to old and rare books. The story follows Shinokawa Tobirako, a high school sophomore and the daughter of the bookstore's owner, Shioriko. Tobirako begins helping with the shop's special consultations, stepping into a world where each antiquarian book carries not only its printed words but also the hidden stories and secrets of the people who once owned them.

The series opens in early spring during a light rain, when a new case arrives at the shop: a mysterious collection of roughly one thousand books left behind in another antiquarian bookstore. The intentions of the various people connected to these books are tangled, and it falls to Tobirako to unravel the truth. As she assists with this and subsequent consultations, she crosses paths with Kyoichiro, a young man whose own family history is deeply entwined with the cases. Kyoichiro's father disappeared years ago, leaving behind a pregnant wife, and the unanswered questions of that abandonment resurface when Tobirako and Kyoichiro investigate a series of clues hidden within the books.

The central narrative arc revolves around the disappearance of Kyoichiro's father, Yasuaki, and the thread of clues that lead to the legendary Japanese novel Dogura Magura by Yumeno Kyusaku, one of the three great strange books of Japan. As Tobirako and Kyoichiro delve deeper, they sense a connection between the twisted narrative of Dogura Magura and Yasuaki's vanishing. The investigation grows more complex when Kyoichiro's grandfather, Sugio, reappears and reveals that a reprint edition from Yasuaki's book collection has had its contents secretly replaced with a first-edition copy. This discovery pushes Tobirako to piece together the motives of those involved and uncover the truth of the past. The story is a bibliomystery that weaves together the love of old books, the weight of family secrets, and the determination of a young woman who uses her knowledge and sharp intuition to solve the puzzles left behind in the pages of forgotten volumes.