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Melinda Sordino begins her freshman year at Merryweather High depressed and alone. Throughout the day, students bully and isolate her. Her former best friend, Rachel, is particularly cruel. The only person who will talk to her is Heather, an annoying new girl in town who is focused on social advancement. Cynical but perceptive, Melinda mocks every aspect of Merryweather. She only becomes excited in the art room, where the passionate Mr. Freeman tells his students that they will each spend the year on a single subject; Melinda gets a tree.

Melinda’ describes her workaholic mother and disinterested father. She discusses her hatred for her babyish bedroom, decorated when she was in fifth grade. In the bedroom, Melinda hides her mirror; she loathes her appearance, especially her raw, bitten lips.

In the following weeks, Melinda has an icy interaction with Rachel, spends time with Heather, works on her tree, and begins to use an old abandoned janitor’s closet in school as a hiding spot. Although she was once “happy” and “driven,” she now feels detached and depressed. This depression worsens when students at a pep rally recognize her as “the one who called the cops at Kyle Rodgers’s party” and torment her.

Heather becomes angry with Melinda for being an unsupportive friend, but quickly apologizes. Meanwhile, Melinda’s parents are upset about her low grades and her apathy. They scold her but end up yelling at each other. In biology class, Melinda encounters David Petrakis, her brilliant lab partner. She continues to pay no attention in her classes, and spends Halloween by herself, remembering when she once had friends.

Heather joins the Marthas, a preppy clique dedicated to community service. Although Melinda helps Heather with Martha duties, the other girls make fun of her lips, causing Melinda to cry in a bathroom. Even worse, Melinda sees a male student she calls IT in the hallway. She freezes, describing him as “my nightmare.”

Melinda cleans her closet and covers its mirror with a poster of Maya Angelou. She notes that it is growing harder to talk, and is grateful for her closet because it allows her to hide her emotions. In her social studies class, after her bullying teacher Mr. Neck goes on a racist rant, David Petrakis begins to protest for his own freedom of speech.

On Thanksgiving, Melinda’s mother tries and fails to cook a turkey (which she forgot to defrost). Her father can’t cook the bird either, and after fighting, the family eats pizza. The next day, Melinda creates a sculpture using the turkey’s bones. Mr. Freeman approves of the piece, as does Melinda’s artistic former friend, Ivy.

School continues, bringing an apple dissection in biology (Melinda flashes back to a childhood memory in an apple orchard) and more protests from David in social studies. As winter break starts, Melinda feels nostalgic for her childhood. On Christmas, Melinda’s parents give her a sketchpad and charcoals because they’ve noticed her drawing. Touched, Melinda almost tells them her secret, but cannot. In the following days of winter break, she’s forced to work at both her mother’s and her father’s jobs.

School starts and Melinda struggles with her tree. She helps Heather with a Martha poster project, and faints during a frog dissection in biology (after identifying with the dead frog). Heather, having been hired as a model, asks Melinda to hang posters; as she does, Melinda encounters IT, who whispers “Freshmeat” in her ear as she stands frozen.

Hearing about her terrible grades, Melinda’s parents scream at her. Melinda refuses to speak, and spends the night in her bedroom closet, scratching at her wrist with a paperclip until blood appears. Matters grow even worse when IT—a senior named Andy Evans—begins to flirt with one of the Marthas, harassing Melinda as he does so.

Melinda continues to earn terrible grades, and makes no progress on her tree. After missing her school bus one day, she walks toward school only to see Andy, who once again targets her. She remains frozen and then runs away from him, after which she decides to cut school, spending the day in the warm, sunny mall.

School continues. Melinda’s English class discusses symbolism in The Scarlet Letter, and she tries to work on her tree. She becomes deeply depressed after Heather decides to stop being friends with her, telling her that she needs “professional help.” On Valentine’s Day, Melinda receives a valentine that she hopes and fears might be from David Petrakis. It is actually a friendship breakup valentine from Heather, which causes Melinda to break down in her closet. She cuts school and ends up hiding in a hospital.

Furious about her terrible grades, Melinda’s parents have a dysfunctional meeting with her principal (whom she names Principal Principal) and her guidance counselor. She remains silent as the adults argue, and is forced to attend in-school suspension. Andy Evans is there, and blows in her ear. She fantasizes about killing him.

On a positive note, Melinda is inspired by the fractured work of Pablo Picasso in art class. One day when she needs a ride to meet her mother, Mr. Freeman drives her, and tells her that she needs to use her tree to express her emotions. She also actually studies for a biology test about seeds, even though she is increasingly depressed by her friendlessness. After sleeping too long in her janitor’s close, Melinda catches the final seconds of a winning basketball game. In the happy hubbub afterwards, David Petrakis asks her to come over to his house for pizza, but she panics and declines.

After a night of insomnia, Melinda climbs to her roof and flashes back to the night of Kyle Rodger’s party; sneaking in with her group of friends, downing three beers to keep from feeling awkward, wandering off into the trees, and being asked to dance by Andy. She recalls him kissing her and becoming more aggressive, and as her memories become fractured, remembers how he suddenly was on top of her, and how she tried to say no until he covered her mouth with his hands. Barely coherent, she recounts how he raped her, and how she dialed 911 afterwards but was unable to make a sound. As she flashes back to the present, she finds that she has bitten through her own lip.

As winter turns to spring, Melinda has a positive interaction with Ivy, but finds out that Rachel and Andy are dating. Horrified, she writes an unsigned warning note to Rachel. In social studies, she turns in an extra-credit report on the suffragettes and becomes excited about the topic, until Mr. Neck tells her that she must read it aloud in front of the class. She and David come up with a plan, and Melinda protests for her right to silence (though David feels she should fight for her right to speak).

As Melinda works in the art room, Andy comes in looking for Rachel, and Melinda is once again unable to speak as he approaches. Ivy comes in during the encounter, and calls Andy bad news. The next day, Melinda wakes up with a fever, and imagines being on Oprah and talking about her rape.

It is May at last, and Melinda begins gardening. She and Ivy, meanwhile, name Andy Evans a guy “to stay away from” in marker on a bathroom wall. Melinda gets stronger, and even rejects Heather when her two-faced friend comes to ask for help making prom decorations. Feeling empowered, Melinda decides to talk to Rachel; the interaction goes well, up until the moment when Melinda tells Rachel that she was raped at the beginning of the year. Rachel is at first horrified and concerned, but reacts with disbelief and cruelty when Melinda reveals that Andy was the perpetrator. Although deeply upset, Melinda becomes happier when Ivy shows her that many girls have added additional warnings about Andy to the wall.

After watching arborists prune a tree in her yard, Melinda goes to visit the place where she was raped; in the quiet grove, she vows to nurture her old self like a seed, hoping that she will soon be able to grow once again. She spends a night with her parents without fighting, and then finds out that Rachel broke up with Andy at prom. Melinda is ecstatic, and decides that she doesn’t need to spend time in her closet anymore.

Melinda goes to clean out her closet, but Andy Evans follows her in. He calls her ugly and jealous, and tells her that she’s lying about her rape. He then vows to give her what she wants, and attempts to rape her a second time. As he goes to unzip his jeans, Melinda screams “no.” She uses her turkey sculpture to break the closet’s hidden mirror, and holds a broken shard to his neck, leaving him speechless and terrified. As she does so, the entire girls’ lacrosse team breaks down the closet door.

School is close to ending, and a summer school-bound Melinda suddenly finds herself popular because of the attack. She sits in the art room and at last creates an imperfect but beautiful tree. As she does so, she admits to herself that her rape happened, but that she will survive it. She then adds birds to her tree, and begins to cry. As she does so, Mr. Freeman comes over and remarks that she’s been through a lot. Melinda feels as though the ice in her throat is melting, and replies, “Let me tell you all about it.”