A flashback is shown with Yu, Yuko, and Kuze in their younger days as high school students. At this time, Yu and Yuko have not seen each other for ten years. In the present day, Mizuki is staying over at Renji's for the time being until she enters high school, and does not have much to do while Renji studies for exams. Renji's mother introduces Kuze to Mizuki, who discovers some of the things Renji was trying to warn her about him might be true. Mizuki and Kuze spend the rest of the day together, and the two become more familiar with each other.
Yu and Yuko originally met at an orphanage twenty years prior. Yu had lost his younger sister in a fire, and continued to be troubled by it for years. Once in high school, Yuko confesses that Yu was her first love, and she still loves him. In the present, Mizuki comes over to Kuze's and he helps her with some laundry. Kuze later collapses in Mizuki's presence, and she makes sure that he is comfortable while he sleeps it off. That night, Mizuki comes over again because she cannot sleep and tells him how touched she was after listening to the CD of Kuze's violin music he gave her. Before she leaves, she tells him that she has fallen in love with him.
In the past, Yuko is going through some "medium-level" bullying as she calls it, but while she does not think anything of it, Yu is very concerned about it. He even asks Kuze to keep on eye on Yuko when she is in class. In the present, Mizuki goes to Kuze's house, but he does not answer, causing her to think he is somewhere else and avoiding her. Mizuki goes to the old train station and talks with Chihiro and learns that Kuze will die soon due to a rare form of neurosis. That night, Chihiro tells her that Kuze is at the beach playing the violin, and she runs to the shore to meet him. Kuze attempts to light his violin and its case on fire, but Mizuki manage to put it out in time, though not before burning her right palm.
In the past, Yu and Yuko go out together to buy new boots for Yuko, and while Yu does not consider this a date, Yuko and her elder brother do; after Nagi catches wind of this, she confronts Yu about it. In the present, Nagi helps Hiro draw his manga in order to beat the deadline, and Miyako makes dinner for him. Mizuki gets a cold and Kuze comes to pay her a visit. After she gets better, the two go out to the surrounding countryside and spend the rest of the day together with Kuze resting his head on Mizuki's lap. Kuze tells her that before he dies he wants to end all relationships, and even though he too has come to love Mizuki, he tells her to never appear before him again.
In the past, Yuko continues to go through being bullied, and this time she fights back, but gets injured in the process. Yu starts worrying about her more, and is angered that her older brother does nothing to help Yuko. In the present, Kei has a talk with Kyosuke about Chihiro, and he suggests that she go and visit it her. When they meet again for the first time in five years, they make amends with the past, and reflect on their futures with those they love. Mizuki wants to be stronger like Chihiro and Kei, but does not know how. When Mizuki expresses this doubt to Nagi, Nagi reveals that she is in fact going out with Kuze.
In the past, Yu finally comes to terms with his love for Yuko, but must turn down Nagi first. After Kuze plays his violin for Yu and Yuko, Yuko starts crying because the music is so beautiful and runs out of the room; Yu chases after her to the school roof. There, Yu professes full devotion to Yuko, and she finally reveals to him what she has been hiding this whole time. Her older adoptive brother has been physically abusing Yuko for years, and she infers that this could have all been avoided had Yu merely said he wanted a younger sister back when they were at the orphanage together.
In the past, Yuko reveals to Yu a knife she always carries given to her by her older brother if she wanted to kill him. Yu takes the knife and confronts Yuko's brother, but Yu does not go through with it, and gets beat up. In the present, Mizuki seeks advice from Kei and Yu on how to approach Kuze, but when she goes to his house, he acts very negatively towards her, and berates her with many questions. After she leaves, Kuze experiences intense chest pains, and after struggling with his pills, and managing to break the bottle open, he takes some of the pills and recovers from the attack while saying he still wants to live.
In the past, Yu and Yuko run away together and eventually find a place to stay while Yu works. Yu runs into Yuko's brother one day and Yu stays out late that night thinking about what he said to him which causes Yuko to worry and go out looking for him. Yuko runs into her brother and he asks her if she wants to go home, and she nods in agreement. In the present, Yu and Nagi talk with Kuze, and try to make him see reason, but he only serves to get Yu and Nagi angry at him for what he says. Nagi tells Mizuki that she is probably the only one left who can save Kuze.
In the past, Yuko is back at school while Yu is still missing. Both of them realize their love for each other, and are helplessly in love. At home, Yuko's brother goes on a rampage and throws Yuko onto the wall, where Yu intervenes and is beaten by Yuko's brother. Yuko's brother takes a look at Yu's sketchbook and takes it with him into his room, where he goes insane and starts drawing his deceased sister. He burns the drawings along with himself. In the present, Mizuki receives charms from Chihiro and Kei, which are keys to the roofs of the two Otowa Academies. Kuze realizes that he wants to live and that now he is all alone.
In the past, Yuko and Yu are now living together again. Yu is getting drawing lessons from Nagi. Yuko meets an orphaned girl named Miki, who was intended to commit suicide with her parents. Soon, Yuko and Miki become friends. Miki meets the young Kuze, and Kuze gives her his green ribbon, which he uses to tie a side ponytail on her. Yu and Yuuko decide to meet after Yu's work on Christmas, but before Yu gets there, Yuko gets into a car accident. By the time Yu and Miki arrive, Yuko is already dead. Yu remembers that Yuko gave him the key to the school roof to keep for safe keeping, and how she said to give it to anyone who is sad or lonely.
In the present, Kuze receives a letter of challenge from Mizuki which draws him out of his home to the Otowa Academy school roof to meet Mizuki. Through her professing words of love to Kuze, he finally gives in and wants to stay in love with Mizuki, but his heart gives out again. Mizuki receives emotional support from Kei, Chihiro and Hiro during this time. Kuze decides to have the risky surgery to try to live longer with Mizuki.
Everyone is spending time with their loved ones during Christmas, whether in Japan or Australia. Kuze survived the surgery and continues to live on with Mizuki. Yu hears from Nagi that Hiro said he talked with Yuko, and Yu heads back to Japan to meet up with her in the church. The two spend the rest of the night together, first at the church, and then at the school's roof to watch the sunrise. Yu and Yuko say their goodbyes and Yuko disappears, leaving behind a white feather.