Melinda Sordino begins her freshman year at Merryweather High School in Syracuse, New York, with a heavy secret weighing on her. Over the summer, she and her friends went to a party and Melinda ended up calling the police, causing her friends and everyone at the party to socially reject her. Melinda's only friend is Heather, a new student, who tries to get Melinda involved in her schemes to gain popularity.
Melinda, however, is not interested in gaining popularity and spends much of her time in an abandoned janitor's closet at school. She has stolen some late passes, so she uses the closet as a hideout to avoid teachers she dislikes and painful interactions with her former friends. Her only solace at school is art class, where she is working on a year-long project to create various interpretations of a tree. In the school hallways, she occasionally sees IT, a name she has given to senior Andy Evans, and she slowly begins to face what he did to her. Whenever he sees her, he antagonizes her in ways that make her relive her initial experience with him. She grows more despondent and even ditches whole days of school. Her parents and guidance counselor try to get her to open up about her poor academic performance, but Melinda refuses to speak to them. However, over many months of painful silence and self-harm in the form of lip- and nail-biting, Melinda finally admits to herself that Andy Evans raped her at the party last summer.
After facing the fact that she was raped, Melinda begins to recover from the trauma of the event. She is worried about Andy Evans' intentions for her former best friend, Rachel, and finally tells Rachel what happened to her. While Rachel does not believe Melinda, Melinda begins to feel free after speaking up. She takes up new hobbies, like yard work, and gains confidence in her attempts at creating a vibrant tree for art class. She no longer relies on Heather's false friendship and begins to reconnect with her former friend Ivy. As the school year comes to an end, Melinda is forced to confront Andy once again when he corners her in her janitor's closet. She defends herself and gains the respect of the school as many other girls have also suffered Andy's attacks silently. She ends the year by finishing her tree and sharing what has happened to her with her art teacher, Mr. Freeman.