After summer break, middle school student Lee So-ri transfers to a rural school in the countryside where her grandmother lives. She carries trauma from her previous school, where she was bullied alongside a friend named Ji-min after standing up to a group of bullies. At her new school, So-ri struggles to open up to others, haunted by her past. On her first day, she discovers a handwritten letter taped to the underside of her desk. The letter warmly introduces the school, the teachers, and the classmates, and hints at the location of a second letter.

So-ri follows the clues and finds a series of letters hidden throughout the school, each leading to the next. The letters were written by a boy named Jeong Ho-yeon, who previously sat at her desk. Through the hunt, So-ri becomes curious about the mysterious sender. She repeatedly crosses paths with Park Dong-soon, a quiet and seemingly aloof classmate who eventually admits he was Ho-yeon's closest friend. Dong-soon had felt abandoned when Ho-yeon left without saying goodbye, but the letters help him realize Ho-yeon did not intend to hurt him. So-ri and Dong-soon begin searching for the letters together, forming a friendship.

The school setting includes memorable locations such as the library, an old flower garden known as the witch's house, a rabbit hutch, and an abandoned bus. A subplot involves a bully named Ahn Seung-kyu, who targets Dong-soon and attempts to use a leaked exam paper to manipulate So-ri and Dong-soon into giving him the letters. So-ri initially hesitates to stand up to him, fearing a repeat of her earlier trauma, but a letter from her friend Ji-min, who also found the courage to resist bullies at her new school, gives So-ri the resolve to act. She and Dong-soon outmaneuver Seung-kyu by recording his confession to arson and exposing him.

As the search continues, So-ri and Dong-soon learn the truth about Ho-yeon: he did not transfer schools but left due to a recurrence of a serious childhood illness, requiring surgery. Ho-yeon had been too afraid to tell Dong-soon, not wanting to burden him. The final letter leads the pair to a train station, where they find Ho-yeon waiting in a wheelchair. Ho-yeon had known So-ri years earlier when they were both patients in the same hospital, and she had been kind to him when he was lonely. Upon learning that So-ri would transfer to his old school, he left the letters to help her adjust and reconnect her with Dong-soon, hoping his two friends would find each other. The story concludes with the three friends reunited.