"Prison School" is set at Hachimitsu Academy, a formerly all-girls school that has recently begun admitting male students. The narrative centers on five male students—Kiyoshi, Gakuto, Shingo, Andre, and Joe—who become the first boys enrolled in the institution. The school is governed by a strict and oppressive student council, led by President Mari Kurihara and her vice president, Meiko Shiraki. The boys quickly find themselves at odds with the council after being caught attempting to peep into the girls' bathhouse. As punishment, they are imprisoned in the school's underground detention facility, where they endure harsh treatment and absurdly exaggerated disciplinary measures.

The story unfolds as the boys navigate their imprisonment, devising various schemes to escape or reduce their sentences. Kiyoshi, the de facto leader of the group, becomes entangled in a complex relationship with Chiyo, Mari's younger sister, who is unaware of his predicament. Meanwhile, Gakuto, the most level-headed of the group, often clashes with the impulsive and reckless Joe, while Shingo and Andre struggle with their own personal quirks and vulnerabilities. The boys' attempts to outwit the student council are frequently met with failure, leading to increasingly comedic and over-the-top situations.

The student council, particularly Meiko, employs extreme and often bizarre methods to enforce discipline, including physical punishment and psychological manipulation. Mari, driven by a desire to maintain order and uphold the school's reputation, becomes increasingly ruthless in her efforts to control the boys. However, cracks in the council's unity begin to surface, particularly as Meiko's loyalty to Mari is tested and her own vulnerabilities are exposed.

As the series progresses, the boys' imprisonment becomes a catalyst for a series of escalating conflicts, alliances, and betrayals. The narrative balances absurd humor with moments of tension, exploring themes of power dynamics, loyalty, and the absurdity of authority. The characters' interactions are marked by exaggerated reactions and physical comedy, often pushing the boundaries of absurdity while maintaining a coherent, if unconventional, storyline.

"Prison School" is characterized by its blend of raunchy humor, over-the-top scenarios, and a satirical take on institutional authority. The series delves into the absurdities of its premise while maintaining a focus on the characters' struggles and relationships, creating a narrative that is both comedic and engaging.