Melancholy, unmotivated Ayanokoji Kiyotaka attends his first day at Tokyo Metropoiltan Advanced Nuturing High School, a government-established institution for training a generation of Japan's best and brightest. In this school, it is said, everything is decided based on merit, which includes the generous monthly "point" allowance students can spend at local shops. As Ayanokoji begins navigating this system, he also nurtures curious relationships with aloof fellow outsider Horikita Suzune and the terminally gregarious Kushida Kikyo.

With their first midterm exam approaching, Class D needs to find a way to improve their class average, or face another month with no points to spend. Even Horikita decides to take part, forming a study group to help the class underachievers. But can the stanoffish Horikita really inspire her classmates to succeed?

Thanks to a lot of hard work and scheming, Class D managed to get surprisingly high scores on their midterm exam. But when a student fails a single test, Ayanokoji makes one final play to save his classmate from expulsion.

Sudo has been accused of fighting with a student from Class C, and depending on an upcoming ruling, Class D might have its few remaining points stripped away.

With the hearing for the assault approaching, Ayanokoji and Kushida attempt to secure the cooperation of Sakura Airi, possibly the only person who can testify that Sudo was acting in self defense.

Sakura's testimony has bought Class D time, but Horikita and Ayanokoji still need to find a way to tilt things in their favor. Meanwhile, Sakura senses the presence of a strange man nearby.