Japanese teenager Shōya Ishida sets his affairs in order and walks to a bridge, intending to commit suicide. Coming to his senses at the last minute, he hears fireworks as he recalls his days in elementary school and the events that have led him to this point in his life.
In those days, Shōya was an indifferent child, one who viewed his fellow students as a way of staving off his boredom. The entry of a new student named Shōko Nishimiya into his class piques his interest when she informs the class that she is deaf. She tries her best to live normally and integrate with the class. However, Shōya and Naoka Ueno found her to be extremely irritating with her communication notebook and they start to bully her viciously. Shōya often plays with her hearing aids and throws them away while Ueno would talk behind Nishimiya's back.
When word of the bullying reaches the principal, Shōya is singled out as the culprit. He names his friends as accomplices, but they turn on him, denying their involvement. Soon, the class's bullying is directed toward him, subjecting him to the same treatment he gave to Shōko. Shōya blames Shōko and the two get into a physical altercation after he finds her doing something to his desk. She is subsequently transferred to another school, and he discovers that she was erasing hateful messages his classmates left in chalk on his desk. Shōya finds himself alone, relegated to the role of a tormented outcast. After being thrown in a pond by his classmates, he finds Shōko's notebook and kept it.
Now in high school, Shōya remains a social reject, having grown to accept his past as punishment. Full of guilt and anxiety, he blocks out the faces of those around him, unable to look them in the eye. Despite his isolation, Tomohiro Nagatsuka, another loner, befriends him and quickly comes to consider him his best friend. Shōya visits the sign language center to return Shōko's once-waterlogged notebook in the hopes of making amends. The two begin meeting at a bridge to feed bread to koi.
Yuzuru, Shōko's younger sister, strongly doubts Shōya's intentions. One day, Shōya jumps into a river after Shōko does the same to retrieve the notebook they both dropped, which happens to be prohibited. Yuzuru secretly takes a photo of Shōya jumping in, and posts it online. Shōya is suspended for the act. Yuzuru reveals that she was responsible, first to Shōko who yelled at her and Yuzuru ran away for the night. Instead of getting angry, Shōya brings her to stay at his house. When she leaves in the middle of the night, Shōya follows and tells her that he is genuinely remorseful for the way he treated Shōko. The sisters' mother, Yaeko, however, is still very resentful and slaps Shōya's face before bringing Yuzuru inside.
Shōko soon gives Shōya a gift and confesses her feelings for him, but because she tries to verbally communicate her affections rather than signing it out, Shōya does not understand her. Worried that the misunderstanding upset her, Shōya invites her to go to an amusement park with him and his group of classmates with Yuzuru's encouragement. There, Naoka tries to reconnect Shōya with an old friend who shrugs him off, but he is intimidated and tells her that he isn't interested. In revenge, Naoka drags Shōko into a ferris wheel but not before Yuzuru hands her the camera with the recording on. She finally voices her feelings of hatred in secret to Shōko, which Yuzuru later shows to Shōya. In class, desperate to remain blameless for Shōko's bullying, Miki Kawai, another former classmate, exposes Shōya's past to the remaining students who were still oblivious to it, while downplaying her own involvement. The group has a heated confrontation about each member's level of responsibility at the koi bridge, ending with Shōya calling out every one of them for who they really are. Afterwards, he asks Shōko if she wants to go to a "special place" during summer vacation.
Shōya goes back to the bridge to meet Shōko but ends up seeing Yuzuru whose grandmother had just passed recently. To cheer Shōko up after her grandmother's death, Shōya takes her to the countryside, where he begins to understand how much she blames herself for everything that has happened to him. Desperate to reassure and change her mindset, Shōya contrives to regularly meet with the sisters.
During the fireworks festival, Shōko goes home under the guise of finishing some schoolwork. Shōya follows when Yuzuru asks him to get her camera. When he arrives, he finds Shōko standing on the balcony, on the verge of throwing herself to her death. Shōya succeeds in grabbing her and pulls her back up, but he falls over the side into the river and slips into a coma. Yaeko and Yuzuru beg for forgiveness from Shōya's mother. Then Shōko and Yaeko become victims of Naoka's wrath when she heard of the news. To atone for this guilt, Shōko comes to see Naoka and Shōya every night at the hospital.
One night, Shōko dreams of receiving a farewell visit from Shōya. Horrified, she runs to the bridge where they fed the koi and collapses in tears. Shōya, awakening from his coma in a state of panic, stumbles to the bridge himself and finds her there, huddled in despair. He formally apologizes to her for the way he treated her, and for the many things he did which may have caused her to hate herself. He asks her to stop blaming herself, and also admits that, while he once considered giving up himself and ending his own life, he has since decided against it. Shōya then asks her to help him continue to live.
When Shōya goes to the school festival with Shōko, he finds out how much his friends from elementary school still care for him and all of them are reconciled. Afterwards, Shōya requests them that the group should go to the school festival together. During the festival, Shōya finally overcomes his past mistakes and is finally able to look at other people's faces, as he cries and realizes that he has obtained redemption and found forgiveness at last.