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.

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.

Class D has achieved a degree of unity in facing the special test, so Ayanokouji and Horikita head out to see how the other classes are getting along. Class B is working together to make a comfortable life for themselves, while Class A remains secretive.

With the panty thief incident already eroding Class D's trust, Horikita finds her leader key card stolen. While they try to figure out who did it, the base camp is thrown into chaos with a new incident of arson.

Survival test is coming to the end. Things don't look well for 1-D. Key card is stolen. And now Suzune is forced to withdraw due to her sickness. Kiyotaka will try to turn things around.

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.

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

Class D prepares to face their next major challenge, a test called "Paper Shuffle" where the price of failure is expulsion.

Karuizawa, whose cooperative relationship with Ayakoji has ended abruptly, cannot hide her embarrassment at the complete loss of contact with him. As Class D discusses their plans for the future, Ryuen and the other members of Class C appear overbearing.

Ayanokoji's class embarks on their first trial as the ascended Class C, the mixed training camp.

Yukimura injures his leg while the group is training for the upcoming tests. He later devises a plan for how the group should handle the marathon and then the day of the four tests arrives.

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...

With the approaching class vote, a disturbing atmosphere hangs over Class C and fills them with suspicion. Second-year Class A's Asahina informs Ayanokoji that Ichinose has asked for cooperation from student council president Nagumo.

Class C considers various strategies for the special exam, but they all lack a decisive factor. Hirata remains disappointed in the class vote result. Ayanokoji calls out to Hirata, who acts coldly towards Mii-chan who is worried about him.

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.