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 are given a high degree of freedom in order to closely mimic real life.

The story follows the perspective of Kiyotaka Ayanokōji, a quiet and unassuming boy, who is not good at making friends and would rather keep his distance, but possesses unrivaled intelligence and incredible physical ability. He is a student of Class-D, which is where the school dumps its inferior students, widely considered "defective". After meeting Suzune Horikita and Kikyō Kushida, two other students in his class, the situation begins to change and he starts to get involved in many affairs, and his thought of an ideal normal high school life begins to get scattered.