In an effort to reduce the likelihood of sexual crimes in Japan, a prestigious all-male school relieves its students using the service of young girls. The reasons these girls are thrown into this unusual career are many, ranging from debt to punishment for crime. Treated as nothing more than government-sponsored commodities, they are stripped of their clothing and identified only by their assigned number.

Nakagawa rarely pays much attention to anyone at school, but that changes when he enters a relationship with the girl known as 'Number 3.' Since personal interactions between the students and the girls are forbidden, the two decide to use the school rooftop as their private meeting place. Spending their days together in secret, Nakagawa begins to learn more about Number 3 as well as the dark truth behind the controversial program.

[Written by MAL Rewrite]