Nanako has her first day at Seiran Academy. Rei helps her on the bus, and Nanako is instantly captivated by her charm. At school, Nanako meets Mariko, who immediately asks her to be her friend. The school listens to a speech by Fukiko about the Sorority and Nanako and Tomoko learn about The Magnificent Ones - Hana no Sainte-Juste (Rei), Kaoru-no-kimi (Kaoru), and Miya-sama (Fukiko).

Mariko looks out for Nanako before class, and shoves Tomoko out of the way when she finds Nanako. Fukiko comes to Nanako's class and announces three Sorority candidates: Mariko, Kaoru, and Nanako. Kaoru declines her candidacy because she is opposed to the very existence of the Sorority, and makes the excuse that she declines due to her poor health. Aya makes a scene, calling Mariko and Nanako unqualified to be in the Sorority, revealing to Mariko that everyone had known all along that she was the daughter of a pornography writer. Aya goes to attack Mariko, but Kaoru stops her. Fukiko gives Nanako the invitation to the Sorority selection party, which clashes with her plans for Tomoko over the weekend.

An insulting note is posted about Nanako's candidacy for the Sorority on the school bulletin board, announcing to the entire school that Professor Misonoo is not really her father. Nanako considers not going to the party, but Tomoko talks her out of it. The day before the selection party, Aya, claiming to be Fukiko, phones and leaves a message for Nanako that the party has been changed to a later time.

Despite missing the selection party, Nanako has her interview, and humiliates herself. Mariko and Nanako realize that anyone could have left the message for Nanako, but Mariko correctly suspects Aya. Nanako and Mariko are notified of their selection to be in the Sorority, and Aya steps up her campaign of insults, revealing that Nanako's stepfather left his wife and child to marry Nanako's mother, who was a cocktail waitress.

Nanako sees Kaoru stops Rei from taking some pills. Fukiko invites Rei into the Sorority House to help out with work, but intentionally injures her hand. Rei demands that Fukiko bandage her bloodied hand, but Fukiko refuses. Nanako treats Rei's wound, eliciting Fukiko's quiet anger. Nanako is officially inducted into the Sorority, but has a nightmare that night where Fukiko attacks her.

The bullying continues: Nanako's gym uniform is stolen and cut to shreds, and Tomoko won't lend Nanako hers. Kaoru lends Nanako her uniform instead. Nanako is attacked by sophomores who did not make it into the sorority last year. Devastated, she attempts to resign from the Sorority, but Fukiko discourages her from listening to her tormenters and promises that Nanako that she will protect her—but this causes Nanako to remember how Fukiko injured Rei. Afterwards, Nanako goes out to think and bumps into Takehiko. He comforts her and somewhat lifts her spirits.

Depressed from her classmates' bullying, Nanako goes to the school's clock tower to spend some time alone. There, she sees Rei, smoking and throwing knives at a carving of Fukiko in the wall. Terrified but entranced by Rei, Nanako researches the origins of Rei's nickname and learns more about her from Kaoru. They part on good terms, but Aya and her friends begin attacking Nanako as soon as Kaoru leaves. She is rescued by Tomoko who threatens Aya and rekindles her friendship with Nanako.

Mariko tries to warn Tomoko off Nanako again, but Kaoru comes by and stops her. Fukiko invites Aya to the Sorority House and threatens her to stop bullying Nanako. Mariko invites Nanako to her birthday party - it is in a grand hotel room, but the only guests are Mariko's mother and Nanako. They return to Mariko's house, and Mariko and Nanako take a bath together. Mariko then tries to convince Nanako to stay overnight, but Nanako refuses because she'd promised her mother to be home. Mariko becomes upset and threatens to kill Nanako, causing Mariko's mother to restrain her as Nanako runs home.

Kaoru collapses from chest pains, so Nanako tries to fetch painkillers from Rei. Rei doesn't take the situation seriously, so Nanako slaps her. Rei is impressed by her boldness and gives her the painkillers, but Nanako is shocked by the amount of drugs Rei keeps in her pockets and the apparent severity of Kaoru's illness.

Mariko refuses to eat anything until Nanako forgives her, but Nanako is giving her the silent treatment. Kaoru notices Mariko's hunger strike and confronts her about it, angry that anyone would throw their health away when Kaoru herself is so ill. Rei watches Kaoru, Nanako, and Mariko participate in a volleyball game from a balcony, but sees Fukiko glaring at her from a distance and nearly falls off. Mariko faints and is taken to the hospital, where Nanako finally decides to forgive her.

The Sorority members have a special study session at Fukiko's house. Fukiko invites Rei to join them, telling her to wait under the elm tree at five o'clock, but doesn't arrive. Nanako returns to school that night for her notebook, and finds Rei waiting under the tree, soaked from the rain and delirious with fever. Nanako tries to take Rei home, but she resists, unwilling to break her promise to Fukiko. Rei attempts to walk through heavy traffic and jump off a bridge in order to get back to the tree, but Nanako manages to stop her. She finally brings Rei home, but discovers that Rei lives alone in a dark, dreary apartment filled with mirrors. In her delirium, Rei thinks that Nanako is her treasured doll and hugs her.

Nanako calls Kaoru to help take care of Rei. Kaoru arrives at Rei's apartment and slaps and yells at her for her masochistic devotion to Fukiko. She reveals that Rei's bracelet was given to her by Fukiko; she rips it off her wrist and tries to throw it out the window into the river, revealing a deep scar on Rei's wrist. Kaoru is forced to stop when Rei starts throwing knives at her, and Rei takes her bracelet back. Terrified, Nanako wonders whether or not Rei's scar was the result of a suicide attempt. Fukiko calls her to ask why she didn't return to the study group, and Nanako makes up a reasonable excuse. Fukiko pretends to believe her but correctly suspects the truth. She orders Nanako the next day at school not to get too close to Rei. Later, Nanako overhears Kaoru confronting Fukiko over what she'd done to Rei. During the argument, she finds out that Rei and Fukiko are sisters.

Rei is well enough to go back to school. She confronts Fukiko, but is made docile with a few words. Tormented, she retreats to the clock tower and takes a lot of drugs. Looking for Rei, Nanako enters the clock tower, and finds her delusional and hallucinating. Believing Nanako to be Fukiko, Rei reveals that Fukiko had made a pact of double suicide with Rei when they were younger. She attacks Nanako with her knives, thinking that she is Fukiko and has arrived to fulfill that pact.

Nanako desperately tries to escape from Rei, but fails. Rei attempts to stab Nanako several times before regaining her senses and breaking down in tears when she realizes what she is doing. They return to Rei's apartment and make peace. Later, Nanako tries to throw away Rei's drugs, but she catches her and angrily orders her to leave. Nanako goes to the beach and cries, but Rei finds and forgives her. Rei happily returns to school the next day despite the first day of midterms.

A Sorority member named Junko Nakaya fails one of her exams due to having been seriously ill, so Fukiko orders her to resign. Nanako tries to defend Junko, but Fukiko tells Nanako to watch her place, as Fukiko was the one responsible for her admission into the Sorority. Later, Fukiko invites the Sorority to a party on her yacht. She takes back her earlier statement, saying that Nanako was admitted to the Sorority on her own merit. But then she questions Nanako if she knows any men, and when Nanako mentions her "penpal", Fukiko orders her to stop writing to him - or else. Later, Junko speaks to Nanako and tells her that she has decided to resign anyway, but thanks Nanako for trying to help her.

It is Kaoru's first basketball game since her illness, and she is determined to win. Her playing is so great that the entire opposing team is forced to block her. Kaoru is injured during the game and blood spurts from her chest. She begs Rei to take her place in the game, and Rei does so, even though Fukiko had forbidden her from playing basketball ever again. Rei plays to her fullest, and despite losing the game, is more alive and happy then she had been in a while. Nanako realizes that Mariko is in love with Kaoru, and her envies her openness with her emotions.

Nanako realizes that she has fallen in love with Rei, but is too nervous to say anything. One of her letters to her "Brother" end up in Fukiko's possession and she must face her wrath.

After Nanako accidentally misses her bus stop, Rei takes her to the park. The two spend a happy morning together, and in a burst of emotion, Nanako confesses her love.

Rei refuses to react after hearing Nanako's confession and begins to intentionally avoid her, breaking Nanako's heart. Kaoru, sensing Nanako's pain, tells her to give up on Rei, for "her soul is enslaved by a goddess," referring to Fukiko.

Nanako and Tomoko decide to go to Takehiko's university fair. They invite Mariko, but she is reluctant because she thinks the men will corrupt Nanako. Fukiko overhears her brother and Takehiko talking about the fair, and is furious that Nanako is going. She invites Nanako to her house for a tea ceremony on the morning of the fair and locks her in the storage room in order to prevent her leaving, but Kaoru hears Nanako and frees her.

Nanako, Tomoko, and Mariko go the University Fair with Takehiko and Takashi, Fukiko's older brother. Mariko does her best to protect Nanako from the men, but ends up comically failing.

Mariko and Nanako are invited by Fukiko to her country house for the weekend to help her prepare for her birthday party. There, Nanako goes for a walk near the lake and sees Fukiko playing her violin sadly. That night, Nanako can't sleep and sneaks out and finds Fukiko insane and tormented in a room, reciting Shakespeare's Sonnet 18 over and over again. Nanako makes a noise, and Fukiko chases her through the house, but Nanako is not caught. The next day, Nanako questions a maid named Minako about the room - it is Fukiko's old bedroom that has been kept the way it was when she was twelve. Fukiko overhears them talking and fires the maid. Later, Nanako sees Fukiko swimming in the lake, and Fukiko pulls her in. Nanako nearly drowns, but Fukiko comes to her senses and saves her, apologizing that she'd only wanted someone to swim with her. At the end, Nanako re-encounters Minako and she tells her not to worry.

Home from the lake house, Fukiko and Rei visit Ms. Asaka's grave on the anniversary of her death, three years ago. The two are unusually civil; as they part, Fukiko invites Rei to her eighteenth birthday party. The party proceeds uneventfully until Rei, oblivious, plays for Fukiko the violin piece she had earlier played alone in the woods. Incredibly upset at hearing the song, Fukiko cuts the violin strings with a knife, then flees the room, effectively causing a scene. Rei runs after her, confused as to her sister's reaction, believing Fukiko's frequent playing of the song to be out of a fondness for it. Fukiko responds that she hates the piece more than anything else in the world.

Confused by the events of the party, Rei inquires of Takashi as to why the song upset Fukiko. It is revealed that, when Fukiko was twelve and Takashi eighteen, Takashi had brought Takehiko Henmi to visit their lake house. Fukiko had instantly fallen for the young man, and vowedto master a difficult violin piece that she would play solely for him. Due to an emergency, Takehiko was unable to attend. Relaying this story, Takashi realizes hat Fukiko had perhaps fallen in love with Takehiko. Later, Takashi mentions to Fukiko that he spent time with Rei, and that they discussed the events of six years previous. Feeling very emotionally violated, Fukiko leaves the room, to reminisce in private. The love she felt for Takehiko made her happier than anything else. When he failed to appear, her young heart was prematurely crushed, and her faith destroyed. In a fit of passion, she ran out of the room and attempted to drown herself in the lake.

Rei reminisces about the first time she met Fukiko, remembering how, even as a child, her pride had still been admirable. She then overhears two Sorority members telling Nanako to meet Fukiko at the Sorority House suspiciously late at night. Nanako goes, and is shocked and scared to find that Fukiko has put on scarlet lipstick for their private meeting. Fukiko puts make-up on Nanako to make her look like a doll and confesses her love to Nanako. She then asks her to leave Takehiko and be with her, instead. Nanako is frozen with fear by Fukiko's seduction, but Rei bursts in the room and breaks it up before Fukiko goes too far. Enraged that Fukiko could lower herself to such a level, Rei angrily tells Fukiko that she knows Fukiko loves Takehiko, and that she'd admitted Nanako into the Sorority so she could steal her away from him. Fukiko runs out of the room in anger, and Rei tackles Nanako and kisses the ear Fukiko had kissed.

Rei reflects on that double suicide pact that she and Fukiko made shortly after Rei's mother committed suicide, when Rei was soon to be properly adopted by the Ichinomiya family. Fearing any further abandonments by those she loved, Fukiko convinced Rei that they could preserve their happiness in death. Fukiko cut Rei's wrist for her, but was overcome by the horror of what she had done and did not follow on her own, instead panicking and screaming for help as she carried the dying Rei. Both Rei's bracelet and doll were gifts from Fukiko as compensation - presumably due to the perceived singular suicide attempt, Rei was no longer to live with the Ichinomiya family. In the present, Rei confronts Fukiko, saying that she had wished to die not for the sake of their happiness, but instead in response to the pain of losing Takehiko.

Mariko's parents are divorcing and she is traumatized, spending the night at Nanako's home to try coping. Things get even worse because it's almost Mariko's birthday: as she, Nanako and Tomoko are celebrating, they find Mariko's father and his girlfriend (after he had said that he wouldn't be able to meet with her), which makes her run away crying. Mariko returns home and has a fight with her mother over how she never says anything about her father's affair, and at night she seriously ponders cutting her own wrists with a boxcutter. At school, Aya cruelly taunts Mariko, reading a newspaper article about Mariko's father's affair aloud to the classroom, in which Nanako angrily tries to stop her. This pushes the still very unstable Mariko over the edge and she attacks Aya with the same boxcutter she almost used on herself. She runs away from school and is about to jump off from a bridge, but Takashi Ichinomiya grabs her before she can do so.

Everyone desperately looks for the missing Mariko, fearing for the worst. This includes both of Mariko's parents and even Mr. Shinobu's girlfriend, who calls her mother and apologizes. Ultimately, when Takashi manages to help Mariko calm down enough, she returns home. Mariko's father feels extremely guilty for his part on Mariko's emotional instability and attempts to talk to her too, with mixed results. Mariko is suspended and expelled from the Sorority for her attack on Aya. Believing the expulsion to be unfair, Nanako quits the Sorority as well.

At the Student Assembly, Kaoru asks for the abolition of the Sorority. Rei is horrified at first, believing that it would destroy Fukiko's pride, but ultimately decides that she has to learn to live without the Sorority in order to be truly strong. Rei, Kaoru, and Nanako begin collecting signatures for the petition. Two-thirds of the student body need to sign it before they can submit it to the school board.

Two Sorority members, Ogiwara and Komabayashi, persuade Aya's friends, Miyuki and Megumi, to steal and burn the petitions. Rei stops them. Aya intentionally takes the blame to protect the girls, saying that she'd ordered her friends to do so, but not before insulting Nanako once more, making Nanako very angry as she snaps back at Aya. Mariko reminisces their rivalry to Nanako and Tomoko. That night, Aya attempts to drown herself in the ocean, but the three of them save her: Megumi and Miyuki revealed the truth to them and Kaoru, and they've been searching for her. Mariko and Aya rekindle their lost friendship, and Aya signs the petition the next day.

The Sorority members are getting scared as the Petition gains movement and their own members begin signing it. Angered at Fukiko's lack of action of the subject, Ogiwara and Kombayashi decide to take matters into their own hands by confronting Nanako in a broken down building. Nanako alerts Kaoru but goes on her own anyway, and the confrontation gets heated...

Fukiko continues to pretend that nothing is wrong. At the final Sorority meeting, none of the members arrive. Rei attends the meeting instead, and encourages Fukiko to continue with her speech. Fukiko enthusiastically does so, saying that she will never lose her dignity no matter what, impressing Nanako with her pride.

Rei dreams of her mother's death, in which Ms. Asaka reveals that Fukiko is her child as well. She was adopted immediately after her birth, depriving her mother of any chance to be near her. As Ms. Asaka walks into the ocean, she tells Rei to protect her elder sister. In the present, Rei tells Kaoru that she is no longer concerned with preserving Fukiko's pride, seeing that it is still plenty strong on its own. Having been absolved of this worry, she shares that she is feeling better than ever. At the Ichinomiya house, Fukiko receives a call from her father. She is quite friendly with him, and quells any worries of his that the Sorority situation might have upset her. Mr. Ichinomiya also asks after Rei; Takashi is surprised to hear this, but Fukiko tells him that their father is always worried about how Rei is doing.

Nanako waits for Rei to pick her up for their date, but soon, everyone finds out about Rei. Nanako, Tomoko, Fukiko, Kaoru, and Takashi go to the hospital to see Rei's body. The police won't let Takashi and Fukiko take the body to be buried, as she may have committed suicide and they want to investigate. Nanako goes home and cries in her room, phoning Rei's apartment, and her parents discuss Rei. Fukiko receives a bouquet of red roses from Rei and a letter, and when she reads the letter, she cries. The next day at school, the police question the students. Nanako stays at home, but later tells her mother she's going to school. She instead goes to the place Rei died and cries. She sees Kaoru and follows her. Nanako tells Kaoru that Rei had planned to see her the next day, and thus, could not have committed suicide. The police conclude that Rei did not commit suicide, and they tell Takashi and Fukiko about her last moments. Nanako wonders where Rei intended to take her on the date.

The school attends Rei's funeral. Fukiko accepts all of the guests with dignity. Afterwards, she asks for two minutes alone and cries over Rei, telling her that she really did love her, and kisses her. Outside, Nanako hallucinates about Rei, imagining that she turns into a bird and flies away, while Takashi breaks down crying on Takehiko's shoulder. Later that night, she smokes one of Rei's cigarettes, and goes to Rei's apartment, where she finds Fukiko. They stay there until dawn. Nanako takes Rei's doll as a memento of her. Fukiko's chauffeur drives Fukiko and Nanako home. On the way, Fukiko reveals to Nanako that she'd known all along that Rei and Fukiko were full sisters, not half-sisters. Mrs. Ichinomiya had told Fukiko the secret on her death bed. Horrified by the secret of her illegitimate birth, as well as the accompanying realization that Rei was her full sister, Fukiko truly felt guilt for what had transpired between her and her sister in the snow.

Two weeks after Rei dies, it is the summer holidays. Kaoru goes for an examination and is told by her doctor that she needs more tests. She reacts badly, thinking she is going to die. Nanako and Tomoko visit the roadside shrine to Rei, and see Kaoru sitting a short distance away, crying bitterly. Kaoru skips class for over two days, and Nanako realizes that Kaoru is suffering despite all her inner strength. Nanako runs into Takashi and he explains to her that Kaoru and Takehiko were in love, but split up. Kaoru goes to the place she ended her relationship with Takehiko, but he sees her there, so she runs away. At school, Nanako meets Kaoru in the clock tower, and Kaoru tells her that she had breast cancer and got a mastectomy. The little hope present for recovery from a relapse within five years has Kaoru petrified, waiting for a potential axe to fall.

Kaoru tells Nanako that she broke up with Takehiko because of her illness and mastectomy, and that Nanako is really Takehiko's stepsister. Nanako's father tells Nanako that she has a stepbrother, and that he loves his son as much as he loves her. Nanako is relieved and visits Takehiko. She asks him half-jokingly what he would have done if she'd fallen in love with him, and he is flabbergasted. Later that night, Kaoru rings Takehiko and apologizes for telling Nanako that Takehiko is her real brother before hanging up. Takehiko and Kaoru remember a date where they went to the fair and rode on a carousel. Takehiko goes to his father for a reference for his study in Germany, and his father wishes him well.

Takehiko is about to leave for Germany, so Kaoru intends to leave him behind for good. Takehiko, Nanako, and Fukiko try to convince her that Rei would have wanted her to live her life to the fullest. Kaoru ultimately accepts Takehiko's marriage proposal, and the two of them agree to move to Germany together.

Fukiko has a hallucination where Rei encourages her to find true love. Fukiko is tormented, thinking that Takehiko was the only love she'd ever have, and cries in her brother's arms. Kaoru and Takehiko marry and move to Germany. Nanako watches their plane leave and remembers Rei. Two years later, she finds out that Takehiko and a now-healthy Kaoru have a child, and meets a lover of her own.