Daisuke Gōra, an unemployed young man struggling to find direction after university, arrives at a quiet, classic bookshop tucked away in a corner of Kamakura. Tasked by his mother with selling a collection of books left behind by his late grandmother, he steps into the Biblia Antiquarian Bookshop. Among the volumes is a rare, signed first edition of Natsume Sōseki's And Then, a discovery that he hopes might solve his family's financial worries. The shop appears empty at first, but he is eventually greeted by its proprietor, the beautiful yet painfully shy Shioriko Shinokawa, who immediately shows far more interest in the books than in making small talk.

Once Shioriko begins examining the volumes, her demeanor transforms completely. Her severe social anxiety vanishes as she focuses on the printed page, revealing a brilliant mind with an encyclopedic knowledge of antique books and a startling talent for logical deduction. From the condition of a dust jacket, an inscription, or an old bookmark, she can unravel the hidden history and secrets connected to each book. To Daisuke's astonishment, she not only appraises his grandmother's collection but also uses the books to uncover a poignant truth about his past: the reason he has suffered since childhood from a phobia that makes printed words blur and cause him physical dizziness. Intrigued and indebted to her, Daisuke accepts a job as her assistant, becoming the lanky, gentle protector who handles customers and the legwork while she remains buried in her books. Together, this unlikely pair forms a partnership to investigate the "case files" of the old books that people bring to their door.

The mysteries they encounter are rarely violent crimes. Instead, the cases delve into the emotional entanglements and quiet deceptions of everyday life, with each antiquarian book acting as a witness to a forgotten event. A couple fights over an old logic textbook, revealing a decades-old lie born of love and shame. A rare edition of The Complete Works of Shakespeare carries a hidden message that could mend a broken relationship. A seemingly worthless collection of magazines unlocks a story of wartime sacrifice and artistic legacy. As Shioriko and Daisuke delve deeper into these bibliographic puzzles, they encounter an ongoing shadow: a cunning mastermind known as the Numa no Tō (the Bog Mansion’s Master), a twisted reflection of Shioriko herself who seeks to acquire, steal, or destroy precious books for personal gain. This antagonist views Shioriko as his greatest rival, setting the stage for a cat-and-mouse game that runs in the background of their bookish detective work, forcing Daisuke to move beyond his role as a simple assistant to protect the quiet woman who has finally given his life a purpose.