Takuma Hirose, a blind junior-high school student, moves from the city to a rural area to live with his uncle to help relieve him of his blindness. On his first day of school, he starts making friends and the introduction of other classmates, but soon discovers that the girl he sits next to in class, Hayami Kohinata, is subject to constant bullying by a few of her classmates. Takuma tries to protect Hayami in any way he can, but since he is blind he cannot do much for her, which she herself reminds him of. Otoha, a spirit only Takuma can see, gives him the temporary ability to see. He later meets Hayami on the hill with his eyesight healed.

Takuma is shown around town by Hinata and two of her friends, and while out they come across a suspension bridge. Takuma is told that a monster lives on the other side and that he should never cross the bridge. Despite the warning, Takuma crosses the bridge later that day and finds Hayami nude washing in a waterfall, and she later brings him to her home, which consists of two old ropeway gondolas. He soon discovers her poor lifestyle, despite that he tries to help her out. Takuma protects Hayami from being beaten up at school the next day and soon Hinata intervenes, ending the fight and protecting both of them. A flashback is shown where Hayami is being befriended by Hinata, but there was a fire after their meeting and Hinata stopped their friendship. After the fight Takuma follows Hayami to her house where she teaches him how to build a toy windmill.

After the events of the previous night, Hinata comes to meet Takuma so they can walk to school together, but on the way they run into Hayami who had been waiting for Takuma. She tries to take Takuma herself, but Hinata does not let go, leading to the three going to school together. At school, today Takuma's class gets to sketch outside for the day, and during this time Hinata refers to Takuma as the "Destined One" while feeding him an omelette she made. Takuma later discovers that Hinata was once Hayami's good friend, but when he tries to ask Hinata why she acts so distant now, Hinata does not tell him. However, a flashback is shown that explains that Hinata was a daughter to an important class of the village while Hayami was a commoner and Hinata's Grandfather objected to their friendship. Takuma tries to take Hinata to see Hayami, but when they get to the bridge, Hinata kisses Takuma as Hayami looks on.

Takuma, Hinata, Yui, Hamaji, and Maki go to the beach together to have fun, but before long Hamaji's younger sister Yukiji shows up and tries to take Hamaji back home. In the end, Takuma and the others agree to let her stay, though for a while Yukiji attempts to hurt (even kill) Takuma or otherwise separate him from the others due to her love for Hamaji. When Yukiji is confronted by the others about Takuma, she runs away and swims in the sea, but when her leg cramps, it is Takuma who attempts to save her, though he nearly drowns himself. Hamaji has to use CPR to revive Takuma, (strangely in slow motion) and Yukiji thanks Takuma for saving her while he was florid with Hamaji's CPR. While taking a bath, Takuma finally realizes that Hamaji is actually male. Hayami comes to the beach to ask Takuma about his true feelings, but they get interrupted by Hinata.

After the events of the beach trip, Hayami starts to ignore Takuma at school, and Hinata continuously presses Takuma to come along with her. Takuma goes to ask Hamaji about what happened between Hinata and Hayami, and he tells him the whole story. Hinata and Hayami had once been good friends, but Hinata's family and much of the rest of the village burned Hayami's house to the ground, and severed the ties between Hinata and Hayami. Takuma goes to see Hinata at her home and drags her over to when Hayami lives across the bridge. Hinata becomes upset about how she has treated Hayami in the past and apologizes to her in tears. Hayami accepts her as a friend again. After the credits in the omake section, there is a parody of Gundam 00.

Hinata continues to hang out with Hayami and still wants to be friends with her, but the other members of the class are a bit uneasy about the whole situation since Hinata complicates things with her being a member of the Kagura family. However, Yui still loathes Hayami due to Hayami's family abusing their power in the town many years ago, which indirectly caused the death of Yui's grandfather due to sickness. When Yui, Hamaji, and Maki go into town, they run into Takuma, Hinata, and Hayami shopping for clothes together. Yui eventually gets frustrated by the situation and leaves, but drops her wallet, which leads Yui to go through the mountains to get back into town. Hayami goes to look for her alone since she knows the mountain area well, and the two meet up at the ruins of Hayami's former home. Otoha then made a vision of Hayami with her family eating sweet omelettes, Hayami's favorite food, to Yui. The next day at school, Yui starts to show a bit of compassion for Hayami.

It is revealed that Hinata's real name is in fact Hotaru and after her older sister Hinata died many years ago, the Kagura family decided to tell the village that Hotaru had actually died, thus Hotaru took Hinata's place. Hotaru does not want to do this anymore, but her grandfather gets very angry at her for trying to revert to being Hotaru again after so many years. Hotaru's grandfather forbids her from going outside the house for the time being, not even for school. During this time, Hotaru thinks of the past when she was with Hinata. After she receives some class notes from school from her friends, and reads the notes they attached, and finally decides to go to school the following day and she tells everyone that her name is actually Hotaru. Her friends quickly adapt to the change and call her Hotaru now.

Otoha uses her spiritual powers to have Takuma experience a very strange world that contains the same people in the same place, but they have all changed dramatically. Hayami and Hotaru and now living with Takuma as younger sisters not related by blood, Hamaji is Takuma's childhood friend, Yui is an evil magical girl, and Otoha is able to come to school with everyone, plus she is Takuma's fiancé. Otoha tells Takuma how he has to take charge in order for the world to correct itself, though it tires him out to constantly be correcting others regarding their strange behaviors. Eventually, Otoha ends her fun with Takuma and says her goodbye as she disappears before him.

The summer festival in town is coming up and the villagers are starting to bring out decorations covered in bells, which makes Takuma remember about his late-mother's bell. He takes the bell to school, but does not know that there is a tradition in the village for a guy to give a bell to a girl he likes before the summer festival, which causes a few misunderstandings. Some of the villagers burn Hayami's makeshift home, and Takuma takes her in to his house. At night, she presses him to tell her more about his mother, and he finally tells her that she committed suicide. The night of the festival, Hayami goes to meet Takuma on a hill overlooking the village and Takuma confesses his love for her. Hayami accepts him and they kiss in the moonlight.

After Takuma and Hayami become a couple, Takuma starts getting hounded by his friends at school for the details for the summer festival. Takuma and Hayami are told by Hotaru's grandfather that it was Hayami's family that drove Takuma's mother to suicide, which is later confirmed by Takuma's uncle. In the midst of this revelation, Takuma realizes that his vision is starting to blur again, and one day during a typhoon, Takuma voices his frustration to Hayami, which causes her to run outside. She makes it to the bridge with sandbags pilled across it to prevent a flood, and starts attacking it with a sign. Two guys from her class, who had previously beaten up Hayami, find her doing this and start beating her up again.

Hayami manages to escape the beating with Yui's interference, and meets Takuma, who went searching for her. She confronts him on his past, urging him to vent his anger and frustration, and is beaten unconscious by Takuma, who loses consciousness as well. Takuma wakes up, having lost his vision, due to his refusal to forgive and forget, learning that he might never able to see again. He becomes introverted, believing everything he experienced was an illusion. Hayami decides to leave the village, but is stopped by the village elder and two others, who intend to kill her. After a brief conversation Hotaru's grandfather fired a shot towards Hayami.

Takuma redirected the gun, calling Hayami his mom, and is able to save Hayami. Following after Takuma, Hotaru arrives with the police to arrest her grandfather and his supporters. Takuma suffers from a mental trauma that causes his mind to return to his childhood stage…to the time when his mother was still alive. He now thinks that Hayami is his mother. Hayami and Takuma is to return to Takuma’s old home where he and his real mother once lived because the doctor recommended that it is best for Takuma to be living in the same environment that his mental state is in. The life of Hayami being Takuma’s mother goes on, while Takuma still have bits and pieces of memories of the true Hayami. While returning from the grocery store Takuma and Hayami came upon a railroad track, Hayami unintentionally creates a scene of the past as a kid runs by them towards the railroad.