"Prison School" is set at Hachimitsu Academy, a formerly all-girls school that has recently opened its doors to male students. The narrative centers on five male students—Kiyoshi, Gakuto, Shingo, Andre, and Joe—who become the first boys admitted to the school. Their excitement is short-lived, as they quickly discover the school's oppressive disciplinary system, enforced by the Underground Student Council (USC), a group of strict and authoritarian female students.

The boys' troubles begin when they attempt to peep on the girls' bathhouse, leading to their arrest by the USC. They are sentenced to imprisonment within the school's prison block, where they endure harsh punishments and humiliating conditions. The USC, led by President Mari Kurihara and her vice president Meiko Shiraki, enforces rigid rules and metes out severe penalties for any infractions. The boys must navigate this brutal environment while devising plans to escape or reduce their sentences.

Kiyoshi, the de facto leader of the group, becomes a central figure in the story as he forms a complex relationship with Chiyo, Mari's younger sister, who is unaware of the boys' predicament. Meanwhile, Gakuto, the most level-headed of the group, often clashes with the USC's enforcer, Hana Midorikawa, whose sadistic tendencies make her a formidable adversary. Shingo, Andre, and Joe each contribute to the group's dynamic, with Shingo's obsession with Mari, Andre's bizarre fetishes, and Joe's quiet resilience adding layers to their collective struggle.

As the boys endure their imprisonment, they uncover secrets about the USC and the school's history, leading to escalating conflicts and alliances. The story balances absurd humor with moments of tension, as the boys' attempts to outwit their captors often backfire, resulting in increasingly outrageous situations. Themes of power dynamics, loyalty, and perseverance are explored through the characters' interactions and the ever-shifting balance of control between the boys and the USC.

The narrative progresses with a mix of comedic and dramatic elements, as the boys' determination to regain their freedom drives the plot forward. Their journey is marked by unexpected twists, alliances, and betrayals, culminating in a climactic showdown that tests their resolve and challenges the authority of the USC. "Prison School" presents a unique blend of over-the-top humor and intense character-driven drama, set against the backdrop of a highly exaggerated and surreal school environment.