The summer before her freshman year of high school, Melinda Sordino meets Andy Evans at a senior party. Outside the woods, Andy rapes her. Melinda calls 911, but does not know what to say and runs home. The police come and break up the party, and some people get arrested. Melinda does not tell anyone what happened to her, and nobody asks. She starts high school at Merryweather High School as an outcast since all her old friends left her, and is shunned by her peers for calling the police. She remains silent and sinks into depression. Melinda is befriended by Heather, a new girl, who clings to Melinda only to ditch her for "the Marthas", who are the "popular" girls at Merryweather High. As Melinda's depression deepens, she begins to skip school, withdrawing from her already distant parents and other authority figures, who see her silence as means of getting "attention". She slowly befriends her lab partner, David Petrakis, who encourages her to speak up for herself.
Near the end of the book, Melinda's best friend Rachel, who was dating Andy, breaks up with him on prom night after Melinda confesses to her what happened. Realizing only one other person could've told Rachel, Andy attacks her in the abandoned janitor's closet, Melinda's "sanctuary". When word spreads about what happened and the truth about that night is revealed, the students no longer treat Melinda as an outcast but as a sort of hero instead. And finally, Melinda tells her story to her art teacher, Mr. Freeman, and the truth finally sets her free.