"High School Mystery: Gakuen Nanafushigi" is a supernatural mystery anime centered around the students of Seimei High School, who become entangled in a series of bizarre and inexplicable events. The story revolves around the "Seven Mysteries of Seimei High," a collection of urban legends and rumors that have long circulated among the student body. These mysteries range from ghostly apparitions to strange phenomena, each tied to a specific location within the school.

The protagonist, Ayumi Kasuga, is a curious and determined first-year student who becomes fascinated by the mysteries after encountering one firsthand. Alongside her classmates, including the skeptical but resourceful Ryoko and the enigmatic upperclassman Tatsuya, Ayumi investigates the origins and truths behind each mystery. As the group delves deeper, they uncover connections between the legends and the school's history, revealing dark secrets and unresolved tragedies.

Each episode typically focuses on one of the seven mysteries, blending elements of horror, suspense, and drama. The narrative gradually builds as the characters piece together clues, often encountering supernatural entities or eerie occurrences that challenge their understanding of reality. The mysteries are not merely random phenomena but are intricately linked to the school's past, involving themes of loss, betrayal, and redemption.

The main characters are developed through their interactions and reactions to the unfolding events. Ayumi's determination and empathy drive the group forward, while Ryoko's logical approach provides balance. Tatsuya, with his mysterious demeanor, often holds key insights into the mysteries, hinting at a deeper connection to the school's secrets. Supporting characters, including teachers and other students, contribute to the atmosphere and occasionally play pivotal roles in resolving the mysteries.

As the series progresses, the investigations reveal a larger, interconnected narrative that ties the seven mysteries together. The final episodes bring the overarching story to a climax, resolving the central enigma while leaving room for reflection on the impact of the events on the characters and the school. The tone remains consistent throughout, blending suspenseful storytelling with moments of emotional depth, making it a compelling exploration of the supernatural within a high school setting.