Six months ago, Lord Hugh Anthony Disward, also known as Huey, lost his eccentric grandfather, Sir Wesley Disward, who was a renowned collector of rare books. His grandfather's will states that, in order to inherit his manor and everything inside it, he must take guardianship over the Bibliotheca Mystica de Dantalian—an archive that contains forbidden knowledge—and also take care of a mysterious girl called Dalian.

As Huey settles into the manor, an old rival of his grandfather's arranges a meeting with him. Dalian, knowing the rival to be Wesley's killer, tags along and discovers that the murderer is in possession of a Phantom Book—a cursed tome that Wesley tried to seal away. When the book puts the two in danger, Huey discovers that the Bibliotheca Mystica de Dantalian and Dalian are one and the same, and she entrusts Huey with the key to unlocking the knowledge stored within her. Together, Dalian and Huey seal the book away, and thus begins an unlikely partnership as they solve mysteries caused by other Phantom Books.