In the not too distant future, the Japanese government has established the Tokyo Metropolitan Advanced Nurturing School, dedicated to instruct and foster the generation of people that will support the country in the future. The students there have the freedom to wear any hairstyle and bring any personal effects they desire.

Our protagonist is Kiyotaka Ayanokōji, a quiet, unassuming boy who is not good at making friends and would rather keep his distance. He is a student of D-class, which is where the school dumps its inferior students in order to ridicule them. After meeting Suzune Horikita and Kikyō Kushida, two other students in his class, Kiyotaka's situation begins to change.