"Jyoshikousei no Koshitsuki" centers on a group of high school girls who attend an elite all-girls academy. The narrative unfolds primarily within the confines of the school, where the students navigate their daily lives, friendships, and the peculiar mysteries surrounding their environment. The story begins with the introduction of the protagonist, a reserved and observant student who becomes intrigued by the enigmatic behaviors of her classmates and the school's staff.

As the plot progresses, subtle hints of supernatural elements emerge, intertwined with the mundane routines of school life. The protagonist discovers that the academy harbors a dark secret tied to its history, involving a series of unexplained events and disappearances. These mysteries are gradually unraveled through the interactions and investigations of the main characters, each of whom possesses distinct personalities and backgrounds that contribute to the unfolding narrative.

The relationships between the characters are central to the story, with themes of trust, loyalty, and the complexities of adolescent friendships playing a significant role. The protagonist forms close bonds with a small group of peers, and together they delve deeper into the school's hidden past. Their journey is marked by moments of tension, discovery, and emotional vulnerability as they confront the unsettling truths that lie beneath the surface of their seemingly ordinary school life.

The narrative structure balances episodic storytelling with an overarching mystery, allowing for both character development and the gradual revelation of the school's secrets. The tone shifts between lighthearted moments of camaraderie and darker, more suspenseful sequences as the stakes escalate. The series maintains a focus on the interplay between the characters' personal growth and their collective efforts to uncover the truth, creating a compelling blend of mystery, drama, and psychological intrigue.