"Gakuen Tokusō Hikaruon" centers on Hikaruon, a high school student who leads a double life as a member of the School Security Force, a secret organization tasked with protecting the school from supernatural threats. The series is set in a world where mysterious creatures and phenomena frequently disrupt the peace of the school. Hikaruon, equipped with advanced technology and combat skills, works alongside a team of fellow students to investigate and neutralize these threats.

The narrative begins with Hikaruon being recruited into the School Security Force after demonstrating exceptional abilities during an incident involving a rogue entity. As the story progresses, Hikaruon and the team uncover a larger conspiracy tied to the origins of these supernatural occurrences. The series explores themes of teamwork, responsibility, and the balance between normal school life and the demands of their secret duties.

Key characters include Hikaruon, the determined and resourceful protagonist; Akira, the tactical leader of the Security Force; and Yumi, a skilled hacker who provides critical support. Each member of the team has a unique skill set that contributes to their missions, and their interactions highlight the challenges of maintaining secrecy while navigating typical high school dynamics.

The plot unfolds through episodic missions interspersed with overarching storylines that delve into the mysteries of the supernatural threats and the true purpose of the School Security Force. The series combines action, suspense, and moments of camaraderie, creating a narrative that balances intense battles with character-driven development. As the team faces increasingly dangerous adversaries, they must also confront personal struggles and the ethical dilemmas of their roles, adding depth to the story.