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.

Classrooms analyze their and others test results. Points distribution is late. Three students from 1-C reported Sudo for attacking them.

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.

Sakura received some weird messages on her portal, than some pictures of herself. Kiyotaka and Suzune are trying to find evidence that would set Sudo free.

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.

All students go to the cruise. Chabashira informs Kiyotaka that somebody requested his expulsion. If he don't help others to promote to A class she will use first opportunity to expel him.

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.

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...

With Day 1 of the "thinking" test over, Ayanokoji is talking to Hirata and the others about a way to break out of the stalemate when he receives a message on his phone from an irritated Horikita. Meanwhile, noticing something strange about Karuizawa's behavior, he seeks information from Horikita, but...

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.

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

Horikita decides to use Paper Shuffle to settle matters with Kushida, and Ayanokoji finds himself caught in the middle.

As the day of the Paper Shuffle draws near, the plans of the various forces in play collide.

Ayanokoji receives a visit from outside the school, and learns more about the conditions of his stay.

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 makes his final decision on how to deal with Ryuen and the Class C threat.

The aftermath of the gymnasium incident plays out as Christmas brings romance to the school.

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.

While Class C are discussing Karuizawa and Hirata's break up Yamauchi is approached by Sakayanagi from Class A. Horikita warns that it's a trap, but Yamauchi pays it no heed. Meanwhile, Horikita tells Ayanokoji that rumors are swirling around Ichinose.

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...

Turns out the one spreading the rumors was Hashimoto, who did so at the behest of Sakayanagi. Shortly thereafter, Sakayanagi appears before Class C and she informs them she has evidence regarding the rumors about Ichinose.

Everyone in Class C has passed their year-end exam. While relief flows through the classroom, Chabashira announces a special exam. It will be a class vote to choose three people worthy of praise and three worthy of censure.

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.

After conversing with her brother Manabu, Horikita offers Yamauchi name as the one who should be expelled. Not only has he made few contributions to the class, but he also worked with Sakayanagi in Class A to expel Ayanokoji.

The class vote has seen the first student expelled from Class C. Sakayanagi meets up with Ayanokoji and they're approached by a man named Tsukishiro sent by Ayanokoji's father. Afterward Ayanokoji challenges Sakayanagi to compete on their next exam.

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.

The class narrowly lost to Class A in the final exam, and were demoted back to Class D. However, the students showed growth throughout the year. Horikita, in particular, having grown as leader requests to dissolve the alliance with Class B.

It's spring break. Shiina calls Ayanokoji to discuss books. Meanwhile, Class B's Kanzaki appears before Ryuen, who is having a secret meeting with Hashimoto. Although the class was defeated, Kanzaki faces Ryuen without hesitation.