Being outcast throughout middle school for his reputation as a bully, Shoya, now in high school, is a depressed loner who is unable to look others in the eyes and envisions an "X" mark over people's faces. To wrap up his loose ends, Shoya goes to return Shoko's notebook at the sign language center and apologize, but then panics and asks to be friends instead. Shoko accepts his offer, leading Shoya to endeavor to make up for his bullying of Shoko. Tomohiro Nagatsuka, another loner, also befriends Shoya after he protects him from a bully.
One day, Shoya accidentally drops Shoko's notebook into a river; he then jumps in to retrieve it, which is prohibited. Yuzuru, Shoko's younger sister, takes a photo of Shoya jumping in and posts it online to get revenge on him, eventually leading to Shoya getting suspended. Shoya finds Yuzuru, who ran away from home, and brings her to stay at his house. When she leaves in the middle of the night, Shoya follows, and the two make up and become friends.
Shoya and Shoko reunite with Miyoko Sahara, a classmate from elementary school who was friendly to Shoko. Shoko later gives Shoya a gift and confesses her feelings for him, but because she tries to speak her affections rather than signing them out, Shoya mishears her.
Shoya invites Shoko to an amusement park with Tomohiro, Miyoko, Miki Kawai (another classmate from elementary school) and Satoshi Mashiba (Miki's friend). There, they are joined by another classmate from elementary school, Naoka Ueno (who had also bullied Shoko alongside Shoya then), who drags Shoko into a ferris wheel. Naoka voices her feelings of hatred for Shoko, blaming her for creating a rift between her and Shoya, with whom she is infatuated. Yuzuru, who had been secretly recording the encounter, shows the video of this to Shoya. Desperate to remain blameless for her part in bullying Shoko following the leak, Miki exposes Shoya's past to the students who were oblivious to it. Later, she attempts to apologize to the group, but Shoya blows everyone off after Naoka remains dismissive.
Shoya learns Shoko and Yuzuru's grandmother died recently. To cheer them up, Shoya takes them to the countryside and sees that Shoko blames herself for everything that has happened to him. Shoya decides to devote his entire social life to the sisters.
During a fireworks festival, Shoko goes home under the guise of finishing homework. Shoya follows when Yuzuru asks him to get her camera. When he arrives, he finds Shoko standing on the balcony, about to commit suicide. Shoya succeeds in grabbing her and pulls her back up, but falls into the river below. He is rescued by his former best friends in elementary school but slips into a coma. Hoping to help Shoya, Shoko meets with each of the group members to explain her and Shoya's situations.
One night, Shoko dreams about receiving a farewell visit from Shoya. Horrified, she runs to the bridge and collapses in tears. Shoya, awakening from his coma, stumbles to the bridge and finds her there. He apologizes for the way he treated her, asking her to stop blaming herself and admits that, while he once considered ending his own life, he has since decided against it. Shoya then asks her to help him continue to live, to which she agrees.
When Shoya returns to school, he is reunited with his friends and comes to understand how much they still care for him. The friends go to the school festival together and Shoya finds he is finally able to look people in the eye again as he envisions the "X" marks falling away. Looking around at his family and all the new friends he has made, Shoya tears up, knowing he has finally redeemed himself.
