"Daimonji to Mondaiji" centers on the life of Daimonji, a high school student who is unexpectedly drawn into a world of supernatural mysteries and puzzles. The narrative begins when Daimonji encounters a series of bizarre incidents at his school, which are linked to a secretive group known as the "Mondaiji." This group, composed of enigmatic individuals with unique abilities, investigates and solves supernatural phenomena that defy conventional explanation. Daimonji, initially a skeptic, is forced to confront the reality of these events after a personal encounter with a supernatural entity.

As the story progresses, Daimonji becomes entangled with the Mondaiji, particularly their leader, a mysterious and highly intelligent girl named Mondaiji. Together, they unravel the truth behind the strange occurrences plaguing their school and the surrounding area. Each case they tackle reveals deeper layers of the supernatural world, often tied to ancient legends, forgotten histories, or unresolved human emotions. The series balances episodic mysteries with an overarching plot that gradually unveils the origins and motivations of the Mondaiji group.

The characters are defined by their distinct personalities and abilities. Daimonji serves as the grounded perspective, often questioning the logic behind the supernatural, while Mondaiji embodies a calm and analytical demeanor, guiding the group with her sharp intellect. Supporting characters, such as other members of the Mondaiji, contribute unique skills and backstories that enrich the narrative. Their interactions and evolving relationships add depth to the story, as they navigate both the challenges of their investigations and the complexities of their personal lives.

The plot is driven by a combination of mystery, suspense, and supernatural elements, with each arc presenting a new puzzle to solve. The series explores themes of human curiosity, the nature of fear, and the boundaries between reality and the unknown. As Daimonji and the Mondaiji delve deeper into their investigations, they uncover secrets that challenge their understanding of the world and force them to confront their own beliefs and limitations. The narrative maintains a steady pace, blending action, intrigue, and character development to create a compelling and cohesive story.