Melancholy, unmotivated Kiyotaka Ayanokouji attends his first day at Tokyo Metropoiltan Advanced Nurturing 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 Ayanokouji begins navigating this system, he also nurtures curious relationships with aloof fellow outsider Suzune Horikita and the terminally gregarious Kikyou Kushida.

1-D learn more about point system. They need to change their habits if they want to score some. But few students don't want to change even if they are facing expulsion.

Kiyotaka explains to Suzune what he did last three days before test. And why everybody get such good scores on tests. But Sudo failed tests anyway and is going to be expelled.

Kiyotaka and Kushida go with Sakura to he mall where Sakura will try to repair her camera. After that Kiyotaka talk to Sakura about Sado's situation and should she talk about what she saw.

Even during summer vacation, lone wolf Horikita would rather remain locked in her room studying than interacting with others. One day, Ayanokouji invites her to visit the pool with some of the others.

As part of a special test, the school has brought the students to an uninhabited tropical island where they must now live for a week. Their performance on the test can have an enormous impact on the point standings of the four classes.

With the island test over, Ayanokoji Kiyotaka and the others are enjoying their summer vacation on a luxury liner. Suddenly, they're interrupted by a new special test. Ayanokoji is called into the same room as Karuizawa Kei and others, where they learn that this test isn't strictly along class lines...

Karuizawa is pushed to her breaking point by the girls of Class C. Ayanokoji watches impassively, but Yukimura flies to her aid, unable to bear it. Noticing Karuizawa's abnormal levels of fear, Ayanokoji seems to get an idea...

At the start of the second term, preparations for the sports festival begin. The students are nervous about the fact that performance in the events will affect their written tests, and even more pressure is added by the unique team breakdowns and freedom given to the students to decide who takes part in what event.

Ayanokoji brings Kushida, whom he suspects of being a traitor, to observe the other classes alongside Horikita. When the day of the festival arrives, Team Red pulls into the lead with great performances by Horikita and Sudo, but Ayanokoji merely watches with disinterest...

As the sports festival comes down to the wire, Horikita must deal with Sudo, as well as Ryuen's threat.

It's Valentine's Day and the boys of Class C are excited about whether or not they will receive chocolates. Meanwhile, Karuizawa seems uneasy over Ayanokoji's request to meet up and while doing so an unexpected person appears...

As Hirata recovers and the class shows unity, it's finally Ayanokoji vs. Sakayanagi. The final special exam has begun and the first round is basketball. Class C puts up a good fight, but Sakayanagi plans to mentally shake Sudo so he will fall.