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Fujimori Gakuen is an elite all-boys boarding school with a unique Princess system: each year three freshmen are chosen to become the school princesses, attending school functions and cheering the clubs and teams dressed as girls to the spirits of the students, who are not able to regularly see girls in the school grounds.

Mikoto Yutaka is one of the chosen for Princess duty in his junior year, along with students Yujiro Shihoudani and Tooru Kouno. At first very contrary to joining the Princess system, Mikoto is eventually convinced by the other Princesses. But just as Mikoto is reluctantly accepting his role, the mysterious Otoya Hanazono transfers into the school. Dissatisfied with the current Princesses' half-hearted efforts and accusing the Student Council of being neglectful of the students' wishes, Otoya creates his own team (the Dark Princesses) to rival the Princesses, and nominates himself candidate for the New School Council.

Mikoto is caught in the fight between Otoya and the current Student Council, unsure of which side to stand for. He also has to deal with his conflicting feelings towards Otoya, and how they affect both his friendship with Yujiro and Tooru and his loyalty to the Princess system. In this process, he comes to understand the true meaning of being a Princess, and finally embraces his role, putting his man's pride aside in favor of the Princesses' pride.