Yunjae is a teenage boy born with Alexithymia — a condition involving dysfunction in the amygdala, the almond-shaped cluster of neurons in the brain. Because he cannot feel emotions, especially fear, his mother Jieun and grandmother try to teach him how to think through and imitate other people’s feelings. Still, Yunjae remains distant and is bullied by his classmates.

Jieun opens a small used bookstore called Jieun’s Bookstore, where the three of them spend most of their time. Their quiet life helps Yunjae make gradual progress in understanding basic emotional responses.

On Christmas Eve, the family goes out to eat. While Yunjae waits at the restaurant counter for candies, his mother is struck on the head with a hammer, and his grandmother is killed with a knife — victims of a random spree killing. Yunjae, unable to feel fear or panic, tries to approach them, but his grandmother shouts for him not to come closer and is murdered before his eyes.

Left alone, Yunjae greets guests at his grandmother’s funeral using the social skills his mother taught him. His mother now lies in a vegetative state in the hospital. Believing she would want him to continue school, he decides to enter high school.
His teacher, well-meaning but lacking empathy, tells the class about Yunjae’s tragedy and asks everyone to be kind. The plan backfires — his classmates begin to bully him and stare at him like a monster.

Yunjae considers closing the bookstore, but Dr. Shim, the baker upstairs and owner of the building, offers help, including financial support. A former medical doctor, Dr. Shim becomes a mentor figure for him.

One day, Professor Yun Kwonho, a business professor, visits the bookstore and asks Yunjae to visit his dying wife in the hospital, pretending to be his long-lost son. His real son, Gon, disappeared at age four in an amusement park and was found only recently. But Gon grew up as a juvenile delinquent who spent time in reformatories, and Professor Yun cannot bring himself to introduce such a son to his dying wife. Remembering his grandmother’s advice, Yunjae agrees to the request. The woman mistakes him for her son, apologizes for losing his hand, hugs him, and dies.

Soon after, Gon transfers to Yunjae’s class after being expelled from a school in Gangnam. He immediately threatens his classmates and notices that Yunjae does not flinch even when beaten. Professor Yun apologizes to Yunjae and arranges a meeting for the two boys at a pizza restaurant. There, Yunjae mimics Gon’s speech and movements exactly — following his grandmother’s advice to imitate when he cannot understand. The imitation enrages Gon, who smashes dishes and demands Yunjae do the same. Instead, Yunjae calls Professor Yun, who arrives, drags his son away, and beats him.

From that strange encounter, Gon becomes curious about Yunjae and begins visiting Jieun’s Bookstore. The two fail to understand each other but gradually develop what could be called a friendship. Gon tells Yunjae about his past and how he was never loved by his parents. One day, he brings a butterfly trapped in a box and challenges Yunjae to feel the sadness of not being able to fly. Yunjae replies honestly that he feels nothing. Furious, Gon throws the butterfly to the ground, killing it, and storms out.

Dora, a girl in Yunjae’s class, loves running, though her father refuses to let her transfer to a school with a running team. When they first meet, Yunjae bluntly asks why she runs — a question she calls the worst, since only her parents ask it. Still, Dora becomes curious about him and begins visiting the bookstore, never explaining her reason. Before long, Yunjae notices a new and unfamiliar symptom: his heart beats faster. Dr. Shim congratulates him, saying his brain is finally forming the neural links that allow him to feel.

Gon sees Dora at the bookstore often and becomes jealous. Having lost the only person he felt comfortable with, he starts causing trouble at school. During a school trip, money goes missing and is found in Gon’s bag. Although he was seen outside at the time, everyone including his father condemns him. Yunjae stays silent, unable to speak up. After being beaten again by his father, Gon joins a gang led by Steel Wire, an alumnus from juvenile detention known for strangling victims with steel wire. Professor Yun later visits Yunjae to apologize but collapses in tears, confessing that he never truly loved his son.

Now able to feel emotion, Yunjae decides to find Gon and bring him back. Dora insists on joining. They locate Gon, but the moment they do, Steel Wire’s gang captures them. Steel Wire orders Gon to kill Yunjae. Gon cannot. Yunjae shouts that Gon is a good person and would never hurt him. Steel Wire stabs Yunjae and flees. In tears, Gon begs Yunjae not to die. Yunjae tells him to apologize — to the butterfly and to everyone he has hurt. Gon does.

Yunjae survives and returns to the bookstore after recovery. Dora transfers to a school with a running team. Gon can now smile at his father. Yunjae has learned to feel, and his mother, now in a wheelchair, tells him that she loves him. Yunjae replies that he loves her too.