"The Mystic Archives of Dantalian" is set in a post-World War I era, blending elements of mystery, fantasy, and historical fiction. The narrative centers on Hugh Anthony Disward, a young nobleman who inherits his grandfather's estate, including a mysterious library known as the Bibliotheca Mystica de Dantalian. This library houses forbidden books known as Phantom Books, which contain supernatural powers and dangerous knowledge. Upon arriving at the estate, Hugh encounters Dalian, a mysterious girl who serves as the "Keykeeper" of the library. She possesses the ability to unlock and control the Phantom Books, and she forms a partnership with Hugh to retrieve and seal away rogue books that threaten the world.

The series unfolds episodically, with each episode focusing on a different Phantom Book and the challenges it presents. Hugh and Dalian travel to various locations, encountering individuals who misuse the books' powers or fall victim to their curses. The Phantom Books often manifest as supernatural phenomena, ranging from illusions and curses to physical transformations, and their misuse typically leads to chaos or tragedy. Hugh, despite his initial reluctance, becomes increasingly involved in resolving these incidents, driven by a sense of duty and a growing bond with Dalian.

Dalian herself is enigmatic, with a sharp wit and a deep understanding of the Phantom Books. Her role as the Keykeeper ties her to the library's history, and her interactions with Hugh reveal glimpses of her past and the responsibilities she bears. The dynamic between the two protagonists is central to the story, balancing moments of lighthearted banter with the gravity of their mission. Supporting characters, such as the eccentric bookseller Flamberge and the enigmatic Rasiel, add depth to the narrative, occasionally aiding or complicating Hugh and Dalian's efforts.

The overarching plot explores themes of knowledge, power, and the consequences of human ambition. The Phantom Books serve as metaphors for the dangers of unchecked curiosity and the ethical dilemmas surrounding the pursuit of forbidden knowledge. As the series progresses, hints of a larger conspiracy involving the Bibliotheca Mystica de Dantalian and its origins emerge, though the focus remains primarily on the episodic adventures of Hugh and Dalian. The blend of historical setting, supernatural elements, and character-driven storytelling creates a unique atmosphere, making "The Mystic Archives of Dantalian" a distinctive entry in the fantasy anime genre.