Kikyō Kushida and Kiyotaka Ayanokōji go through their morning routines to prepare themselves for the bus in anticipation for the upcoming school year. Kiyotaka boards and asks Suzune Horikita if he can take the seat next to her to which she consents. As he wonders if he will be able to make friends in the upcoming school year, Kikyō gets in the bus.
Kiyotaka Ayanokōji is sleeping in class as Suzune Horikita attempts to wakes him. Threatening him with various methods of injury should he not wake up, he quickly reacts to her threats and the two lightly banter with one another. Reflecting on his interaction with her, Kiyotaka regrets his decision of making a deal with Suzune. Time skips back to two months earlier, where Kiyotaka is on the bus heading towards school. An older woman boards the bus but all available seats are taken. A businesswoman and Kikyō Kushida request for student Rokusuke Kōenji to give up his seat to the older woman, to which he declines. Kiyotaka exchanges a quick glance with the girl he is seated next to while thinking about whether he should give his seat up himself.
The bus arrives at Advanced Nurturing High School where the students on the bus depart. As he is walking onto campus, he is stopped by the girl he sat next to on the bus. She inquires about why they exchanged glances, and they begin to discuss the matter of giving up their seats to the older woman on the bus. They both agree that they would not have given up their seat, but the girl insists that they are not of the same mindset. They agree with one another that they would rather not get involved with one another and depart for campus.
Coincidentally, the two of them happen to be seated right next to one another in their classroom, class 1-D. Kiyotaka introduces himself, while the girl unhappily introduces herself as Suzune Horikita. Kiyotaka tells her a bit more about himself, while she stays quiet about herself in response. The atmosphere between the two gets more strained until they notice Rokusuke Kōenji enter their classroom as well, to their mutual disdain.
Later on, their teacher enters the classroom and introduces herself as Sae Chabashira, she informs the students that she will be their teacher for the next three years and hands out some information about the rules and regulations of the school. Kiyotaka reads that students are not allowed to leave campus or contact those outside of the school. Sae then passes out student ID cards and explains that they contain points which are used as money on campus. She then explains students have 100,000 points on the cards already, and that they will receive points monthly until graduation.
After the opening ceremony, Kiyotaka looks around campus and decides to visit the convenience store. He once again meets Suzune who is purchasing supplies for the upcoming school year. After some light back and forth between the two of them, they notice a stand containing items that are marked as free. They dismiss the stand as the school being kind to its students and are immediately interrupted by a student making a scene at the register of the store.
The red-haired male student had forgotten his ID and was unable to pay for the noodles he wanted. Recognizing him as a student from his class, Kiyotaka pays for his noodles. The student introduces himself as Ken Sudō and thanks him for helping him out. The three of them leave the store and talk for a bit until Ken and Suzune get into an argument and Suzune leaves. Kiyotaka and Ken stay behind and talk a bit until a group of second year students come by and put something in Ken's noodles telling them to get out of their spot. After seeing Ken's reaction, they guess that the two of them are students from D-Class, and after verifying this, they leave them alone out of supposed mercy.
Kiyotaka Ayanokōji heads to the dorm rooms for the first time after finishing up at the convenience store. He receives his key-card for his room and after viewing the spacious insides, he relaxes and thinks about his reason for attending Advanced Nurturing High School in the first place: freedom. It is stated that in middle school, he was forbidden to associate with friends or relatives that were not approved for him.
The next day right before lunch, Suzune Horikita and Kiyotaka discuss the value of friendship, with Suzune being adamant that friendship is unneeded. Kiyotaka clearly desires friends, and when Yōsuke Hirata announces that he is going to go get food and asks if anyone would like to join, Kiyotaka almost speaks up but misses his chance to join in. He leaves the classroom himself and is stopped by a cute girl shortly after. She introduces herself as Kikyō Kushida and asks if he is friends with Suzune. He denies this, but Kikyō isn't convinced, bringing up that the two of them were talking on the day of the opening ceremony. She states that her goal is to become friends with everyone in the class, but Suzune had coldly rejected her request to become acquainted. Kiyotaka explains that he had only met her the day before. Accepting this response, the two shake hands and part ways.
Later on in the lunch break, Kiyotaka returns to the Classroom 1-D, where he comes across Suzune eating her own lunch. As they eat in silence, a notification that a exhibition of the schools club activities will be occurring in the gym comes on over the loudspeaker. This prompts Kiyotaka to ask Suzune if she intends to join any clubs, to which she immediately rejects. Kiyotaka explains that he also was not intending on joining any clubs himself, and Suzune realizes that he's only attending to attempt to make friends himself. Gaining some level of interest, she agrees to attend the exhibition with him for a bit.
After school, the duo attend the exhibition together. As the clubs present to the attending students on stage, Kiyotaka and Suzune discuss whether they are interested in attending any of the various clubs that come up. After the event is coming to an end, the final representative comes on stage. Suzune has a visible difference in attitude at seeing the man take the stage, and doesn't respond to Kiyotaka's questioning on the matter. The representative introduces himself as Manabu Horikita, the president of the student council. He explains that the student council is looking for first year students who are not part of any clubs themselves and are motivated for positions.
After the presentation, Suzune leaves on her own while Kiyotaka wonders if the two Horikita's are related to one another. As he is walking to the dorms, Kikyō appears outside the gym and calls out to him. She states that there was something that she would like to talk with him about, to which Kiyotaka agrees to discuss.
In a cafe, Suzune Horikita accuses Kikyō Kushida of setting up a scheme to get them to meet each other. She specifies that the girls who had vacated the table in front of them were girls from class D, as well as the girls at the nearby table. Since she and Kiyotaka Ayanokōji had come to the cafe right after school, the students only being at the cafe for a few minutes doesn't add up to her. Not taking this as a coincidence, she pressures Kikyō for her motive in the situation.
Time skips back to Kikyō and Kiyotaka's meeting the day before after the club exhibition. The two of them go to a bench and Kikyō asks if Kiyotaka had ever seen Suzune smile before. Kiyotaka doesn't believe he should get involved with the situation any more than needed, but as Kikyō explains her unsuccessful attempts to get closer to Suzune, she begins to flirtatiously touch Kiyotaka. As Kiyotaka panics internally, she asks him to help with getting Suzune to open up to her. Still putting up a resistance, he resists her request until she gets really close to him, causing him to fold and agree to help with the situation.
Time skips back to the cafe, where the situation had been explained to Suzune by Kiyotaka. Kikyō pleads with Suzune to become friends with her, where once again Suzune coldly rejects her request, explicitly stating that she does not need or want friends since she considers them unnecessary. The next day, Kiyotaka is thinking back to what Suzune said about the importance of friendship, finding common ground with her opinion and his past experiences. His thoughts are interrupted by Kanji Ike, Haruki Yamauchi, and Ken Sudō calling out to him to get him to come to the swimming class that everyone had already left to go to. The four of them go to the pool where Kanji and Haruki are obsessing over seeing girls in their swimsuits. The topic of their conversation turns to breasts as they discuss who they think has the largest in Class 1-D. They talk about girls for a bit more as Kiyotaka realizes that he's having a conversation with them really easily.
While Kiyotaka is happy about potentially made friends, the girls arrive at the pool. Suzune immediately takes note of Kiyotaka's body shape, and asks him if he does sports. Kiyotaka tells her that he's part of the Go Home Club, but she doesn't accept that response. He dismisses it as simply having good genes. Higashiyama arrives and begins the swim class, announcing that after a warm up, they will be competing with one another in a 50m freestyle race. He mentions that learning to swim will be useful over the summer. After the race, Rokusuke Kōenji easily takes first place in the class as Kiyotaka thinks about what the instructor said about swimming being useful over the summer and what he meant by that.
Class 1-D finishes taking an exam. Kiyotaka Ayanokōji thinks about it for a bit, finding something off because the content seemed misplaced for high school students. After class, Kanji Ike, Haruki Yamauchi, and Ken Sudō meet up with him to question him about the relationship he has with Suzune Horikita, believing that their interactions are proof that the two of them are in a relationship with one another. Kiyotaka quickly denies this and the conversation quickly shifts over to kikyō Kushida. Kanji exclaims his love for her and fights with Haruki about who will get together with her. They grill Ken about his interests make everyone in the group swear to tell everyone else the moment they get into a relationship. On the topic of relationships, they bring up that Yōsuke Hirata and Kei Karuizawa had gotten into a relationship with one another and express their dislike for popular boys and their jealousy for having gotten a girlfriend.
Kiyotaka gets a drink from a vending machine and because Kanji and Haruki had spent most of their points on video games and other things, they ask for him to buy a drink for them as well. While he looks at the vending machines options, he notices that it has a free water option, which causes him to think about how there are free vegetable options available in the cafeteria as well. Kiyotaka gets a bad feeling about how the point system works while the other three exclaim their excitement for getting next month’s points.
Later on after class, Kiyotaka gets invited out on a trip around campus with Kikyō, Kanji, Ken, and Haruki. Agreeing to join up with them, they all meet up in front of the dorms, where Kikyō reveals that she had invited Yōsuke and Kei as well. After some resistance to Yōsuke’s presence, the group leaves for the shopping area. Kanji and Haruki fight over Kikyō while the group talks about relationships for a bit. After everyone is done shopping, the group takes a break and gets some drinks. They talk about the school system, expressing their thoughts on the points they get each month. Kei and Kanji express that they need more points to get everything they want, while Yōsuke and Kikyō express their reservations towards becoming too used to an expensive lifestyle.
Yōsuke asks Kiyotaka his thoughts on the matter, and Kiyotaka explains that he’s suspicious with the entire point system and the school. Haruki agrees and wonders why the school would accept people who are bad at academics like Kei and Kanji, and Yōsuke asserts that the school must be basing things off more than just grades. The group dissolves as people head back to the dorms. The next morning, on the first of the month, Kiyotaka arrives at Class 1-D wondering why the class is so rowdy. Kanji asks him immediately after he enters the classroom if the points had been dispersed to his account this morning, since they hadn’t been dispersed to anyone else’s account yet.
After homeroom, Kiyotaka Ayanokōji was called to the staff room over the loudspeaker by Sae Chabashira. He arrives in the room where he meets Chie Hoshinomiya unexpectedly. She explains that she and Sae are close friends since high school. She asks his name, and proceeds to question him about his popularity. She grabs his arm and flirts with him until Sae arrives in the room and splits them apart. She tells Kiyotaka to come with her to the guidance room, and when Chie attempts to follow along, Sae aggressively tells her to stay at the staff room. Responding this, Chie changes her attitude and accuses Sae of having a goal in mind by inviting Kiyotaka to the staff room. The two face off for a bit until the interaction is interrupted by Honami Ichinose, looking for help with student counsel affairs.
Chie and Honami take their leave as Kiyotaka is led to the guidance room. He is told to stay quietly in the kitchen beside the guidance room under the threat of expulsion and she leaves the room. Alone, Kiyotaka thinks back to what occurred during homeroom, where Sae explained to the class that their excessively poor behaviors over the last month had caused them to lose all of the points that their class had. She had elaborated that performance in class is directly related to how many points the class is given. She went over the point totals for all the classes after the first month, with Class 1-D obtaining a total of 0 points. It was then revealed that the school measures its student’s abilities, and places the students into the class that they deserve to be placed into with D-class being the class where the defective students from the school are placed. Going further into it, she states that the ranking of the classes was based entirely off how many points they have. Sae explained that even if the students stopped being late and talking during class, they wouldn’t be given their class points back.
The results from the exam that they were given a week earlier were posted, and Sae explained that getting a failing grade on any of the exams or tests would result in being expelled immediately. Kiyotaka considers that getting a student expelled would affect whether they would be able to accumulate class points again in the future. He accepts all of this, resolved to simply not get expelled when he hears a voice clearly coming from the other room.
Suzune Horikita stops by the guidance room looking to speak with Sae. She asks why she was placed into D-Class, not believing that she deserved to be placed into the lowest class. Sae brings out her answer sheets for the schools entrance exam, to which she commends her for placing third overall among all the first year students. Suzune asserts that she was incorrectly evaluated once again after hearing this, to which Sae denies, stating that the school does not evaluate its students simply based off their academic abilities, using students like Kanji Ike and Ken Sudō as examples. She then states that there are students who have no desire to rise to the upper classes. As Suzune gets up to leave, Sae reveals that there is another student in the room with them, and threatens for Kiyotaka to reveal himself from the next room.
Kiyotaka comes out and denies having heard anything, but Sae dismisses his denial. Suzune turns to leave the room, but Sae stops her and tells her that overhearing their conversation might help her get to A-class. Sae brings out all of the exams that Kiyotaka has taken so far, bringing up his score of 50 across all tests. Sae asks him what it means, but he dismisses entirely as a coincidence. Sae follows up by showing them his most recent quiz, where Kiyotaka had gotten the hardest question correct through the use of a complicated formula, but had gotten the easiest question incorrect. Kiyotaka continues to dismiss it as a coincidence, while Sae asserts to Suzune that Kiyotaka might even be smarter than she is.
They are dismissed from the guidance room, and Kiyotaka attempts to leave. Suzune stops him and confronts him about what they were just shown. Kiyotaka repeats that it was a coincidence, and asks her about her ambition of reaching A-class. She affirms that it’s her goal to reach class A, but Kiyotaka states that goal is a pain. He brings up the poor results that were gotten by their classmates on the last exam, as well as the poor behavior that the class has been exhibiting since the start of the semester. Suzune expresses her desire to fix these things and come out ahead despite everything, and asks Kiyotaka for help in doing so.
Later on, Kiyotaka, Suzune, Ken, Ike, Haruki Yamauchi, and Kikyō Kushida had met up in the library to study for the upcoming midterm exams. Suzune confronts Kikyō about why she attended the study session, to which she responds stating that she might need some assistance with passing the midterms. Kiyotaka thinks about how it was only with her help that he was able to convince everyone else to even attend the study session while Suzune hesitantly allows for her to attend. Suzune hands out a list of topics and questions that will be on the test. It’s immediately apparent that three boys don’t even understand the content in the questions. Ken expresses his desire to stop studying as Suzune provokes him further, questioning his ability to commit to hard situations. The study group totally fails, and three boys pack up and leave with a frustrated Kikyō departing shortly afterwards.
After the session, Kiyotaka decides to look for Kikyō to thank her for her assistance with setting everything up, and ultimately sees her walking into the school building. He follows afterwards and after he walks in, he hears a loud banging sound happening somewhere in the building. He heads towards the sound and find Kikyō kicking the door in the stairwell while loudly cursing at Suzune, expressing her distaste for her vocally. She turns around to see Kiyotaka and asks him if he had heard anything. He admits that he had heard her and Kikyō directly confronts him and tells him not say anything about this to anyone. She threatens him that she will spread rumors that he had raped her if he doesn’t comply, to which Kiyotaka denies having done. She takes his hand and places it on her breast, stating that she will use these fingerprints as evidence for the police if he ever dares to tell anyone about this, prompting him to agree to her terms.