This story takes place in England after World War I. After the death of his grandfather, Hugh Anthony Disward, also known as Huey, receives a mysterious key and according to his will, must take custody of the Bibliotheca Mystica de Dantalian (The Mystical Library of Dantalian) in order to inherit his estate and all his possessions.

Upon meeting Dalian, a child living on the estate, he learns that she is the guardian of the Archives, which contain forbidden knowledge stored in thousands of magic books called "Phantom Books." Upon agreeing to become Dalian's new Keykeeper, Huey joins her in investigating incidents of people misusing the power of the Phantom Books, most of them with tragic consequences. Using his power as Keykeeper, Huey must seal the power of the Phantom Books and restore order to the world.