High schooler Natsuo is in love with his teacher, Hina. Trying to get past his feelings, Natsuo goes on a group date with his friends and meets a quiet girl named Rui Tachibana. Uninterested in the event, the two sneak out. She takes Natsuo to her house and then asks him to have sex with her, although she is not romantically interested in him. Afterwards, his widower father tells Natsuo that he is going to remarry, and Natsuo finds that his new stepsisters are Hina and Rui. Following the marriage, they move into a new house together. As everyone is going to bed, Natsuo tries to kiss a sleeping Hina but is interrupted by Rui.

Rui drags Hina to her bedroom after seeing Natsuo try to kiss her. The next day, Natsuo finds that Rui has transferred to his school; they decide to act like strangers. Natsuo observes Hina crying on school roof. During lunch, Natsuo helps Rui make friends by staging an argument which allows their classmates to see Rui's personality. Later at home, Natsuo tries to get a reluctant Hina to open up about her boyfriend, but they are interrupted.

Natsuo is upset about Hina's relationship with her boyfriend, and is encouraged by his best friend Fumiya. He asks Hina to break up with her boyfriend, but ends up kissing her. Hina slaps his face, then returns the kiss and pushes him onto her bed. After seeing the shock in his eyes, she tells him that he is still a child and should not interfere in her life. The next day, Natsuo leaves the house to stay with Fumiya, upsetting the household. Rui meets him at Fumiya's house and, after discussing how to break up Hina's relationship, they return home.

Natsuo and Rui stalk Hina, but have no luck finding her boyfriend. They steal Hina's phone, planning for Rui to impersonate Hina and break up, but she is too nervous to speak to the stranger. While they discuss their next move at the restaurant where Fumiya works, Hina and her boyfriend Shuu enter. Natsuo argues with Shuu until Rui throws water in Shuu's face and runs away. Natsuo follows her, and later Hina tells Shuu that they should avoid each other for a while. The next day, Natsuo visits his mother's grave. Rui and Hina follow him, with Hina stating that her relationship is over. They then pray at the grave together, introducing themselves as Natsuo's new sisters.

Rui befriends Momo Kashiwabara, who has a reputation for dating numerous boys. They meet Natsuo while shopping, and he saves Momo from being struck by a bicyclist. Momo later asks Rui is she can fall for him. Momo flirts with Natsuo at school but he returns home to take care of Rui, who said she was sick, and Rui reveals that Momo has a crush on him. The next day at lunchtime, Momo kisses Natsuo on the cheek to cheer him up. Later, Momo invites him to her house where they make out in her room. He sees scars on her wrist, which she tells him to ignore. Natsuo cooks yaki udon for her, telling her that she can call him whenever she is lonely. She begins to cry, telling him how none of the boys that she dated treated her like he does. She asks him if they are dating, but he answers that maybe neither of them should date people they are emotionally dependent upon.

Rui asks Natsuo to help her find a club. They come across the Literature Club, where Natsuo takes a book by his favorite author, You Hasukawa, though Rui warns him about theft. When returning it the following day, he is caught by teacher Reiji Kiriya who threatens to report him if he doesn't join the club. When Kiriya learns that Natsuo and Miu Ashihara, the club's only other member, both like romance novels, he tries to get them to kiss; Natsuo stops after seeing tears well up in Ashihara's eyes. The next day, they begin passing notes in the library, forming a friendship. Momo and Rui later join the club. On the weekend, Hina asks Natsuo if they can go out.

Natsuo and Hina are mistaken for a couple at a restaurant. They talk at a beach, Natsuo being curious about why she had the affair with Shuu; a flashback shows Hina's high school days with him. Natsuo tells Hina that he has finished his novel, and confesses his love for her. He is surprised when she asks if they can go out; she wades into the water with him, explaining that it would be like committing double suicide because they would lose everything. They return home and Hina reads Natsuo's novel. The following night, Natsuo peeks into Hina's room and sees her masturbating while calling Shuu's name. He drops a book and hides behind the stairs when she looks for what caused the noise. The next morning, Hina greets Natsuo and says that he should wake up a little early; she waves to him as she leaves; looking at her hand, Natsuo feels embarrassed.

Natsuo and schoolmate Alex catch a thief who stole Rui's underwear. Alex becomes interested in Rui but when Natsuo introduces them, Rui storms out. Natsuo cooks for Rui to apologize, which she accepts by having him kiss her. Hina sees this and becomes upset, and Rui tells Hina her true feelings. Hina decides to move out. On a family outing to a shrine, Natsuo tries to talk to Hina; she initially tries to avoid him but then confesses her true feelings and how she couldn't hold back if she stayed. They hold hands as they walk home.

Rui meets Shuu at a bookstore; he treats her to a meal to apologize for the trouble he caused, and explains that he is now divorced but would feel selfish to reconcile with Hina. Hina moves out but leaves Natsuo a key to her apartment. Later, Rui finds Natsuo staring out the window in Hina's old room and hugs him. Natsuo goes to Hina's apartment and watches her sleep; she wakes up and he tells her that he is willing to die with her. They kiss, but Hina stops him when he tries to go further, saying that they shouldn't rush things. The next day at school, she confesses that she feels the same way and they kiss.

Natsuo regularly visits Hina's apartment as their relationship progresses. The Literature Club members go to visit absent teacher Kiriya, and at his apartment learn that their club supervisor is novelist You Hasukawa, one of Natsuo's idols. Natsuo breaks his leg and Rui cares for him, including bathing him, but he lies to her about his secret visits to Hina. After being put out by his lies, Rui reads Natsuo's novel and realizes that he is in love with Hina. She confronts him at Hina's apartment and flees when she sees them together. Natsuo finds her, resolving to tell her everything.

Natsuo tells Rui about his relationship with Hina, and Rui decides to shun them while not at home. Rui confronts Hina, who apologizes for her relationship with Natsuo and offers to break up; understanding Hina's feelings, Rui stops her and the sisters reconcile. The second-year students go on a beach vacation to Okinawa, where Natsuo buys a souvenir ring for Hina. When he sneaks into her hotel room to give it to her, she tries to break up with him; Natsuo objects and puts the ring on her finger. They watch a fireworks display from her window and Natsuo asks Hina to marry him in the future, calling her by her name for the first time. They have sex and discuss their feelings. Returning to the school, Hina is summoned by the principal and shown a picture of her kissing Natsuo at the hotel window.

The principal confronts Hina over her relationship with Natsuo. Hina announces that she is being transferred to a distant school. Natsuo and Rui are unable to contact Hina; a letter in Hina's empty apartment explains to Natsuo that she requested the transfer in exchange for the school's silence, and to help Natsuo move on. Natsuo falls into a depression, until members of the Literature Club encourage him and he pours his heart into a new novel. On New Year's Day, Natsuo and the club take it to Kiriya. Later, Natsuo is 'abducted' to a ceremony where his novel, entered into a contest by Kiriya, has won first prize. Natsuo returns home and is surprised when he thinks he sees Hina, rushing to hug her and tell her the news; it is actually Rui in a wig, and she rushes to her room in tears. Natsuo and Rui discuss his feelings for Hina, and he admits to having sex with her. Rui then kisses Natsuo and says she won't hold back any more. Elsewhere, two schoolgirls discuss Hina's hair, which is now short. Hina looks to the distance and smiles as the resolution in Natsuo's second novel, entitled "Well, See You".