Torrey Adams, the narrator, moves to a new town and begins his senior year at Rothborne, a boarding school. As he starts thinking about how his year will be, he remembers how strange his junior year was, in particular, his former classmate Christopher Creed, who disappeared without a trace, except an email to the principal.
Torey, with friends, and big dad reads the email from Chris. It hints at the possibility of either suicide or running away. The email mentions Torey and one of his friends, among other classmates, as guys who have "everything". This makes Torey more concerned about Creed's disappearance and what has become of him.
At school, Torey begins to feel alienated from his friends Alex, Ryan, Renee, and girlfriend Leandra when they joke about Chris's disappearance and seem to take it lightly. The character Ali McDermott is introduced when she talks to Torey about Creed and asks him to come over that night, as she wants to show him something.
At Ali's house, Torey discovers that her home life is awful. He also meets Ali's boyfriend, Bo Richardson. Bo is a "boon" (a somewhat derogatory term in the community that refers to a group of students at their school who come from poorer homes and are avoided by the others, including Torey and his friends) who had injured Chris previously. After introductions the three begin to talk about Chris. Ali's window has a clear view into Chris's bedroom, and she describes seeing Chris hide a diary in a picture frame on the wall, the only place safe from his mother's prying eyes. Ali expresses her suspicions that Mrs. Creed had something to do with her son's disappearance, and the group becomes convinced that the evidence they need will be found in the diary.
Torey comes up with a plan: he will go to a nearby payphone and call the Creeds, demanding that they come meet him and bring money in exchange for information about Chris. Meanwhile, Bo will break in and take the diary. The plan backfires, and all three are brought to police headquarters. Torey's mother, a lawyer, intervenes, saving them from prosecution for the time being. However, Bo confesses to the phone call despite his innocence. Ali and her younger brother, Greg, spend the night at the Adams' house upon Bo's insistence. At the Adams' home Torey's mother hands Ali a notebook that Bo claimed was Ali's. It is actually Chris's diary, that reveals he had a girlfriend named Isabella. Inside the diary Chris wrote that he was afraid that his mother would "kill" him. The diary claims that Isabella is a shy, quiet girl who had a romantic and intimate relationship with Chris over the summer and together they discover from Isabella's Aunt, a psychic, that one of them would die in the woods.
At school the next day, Torey becomes further distanced from his friends. Renee and Ryan question them about Bo Richardson. He successfully avoids his friends but leaves home sick during the school day. Ali comes to his house after school and tells Torey that Bo has been arrested. Leandra calls Torey and when Ali picks up the phone she accuses him of sleeping with Ali. Torey and Ali go to meet Bo, but run into several of Torey's friends, resulting in an altercation, whereupon Bo reveals to Ryan and Renee that their father, chief of police, had cheated on their mother with Mrs. McDermott.
Later, Torey finds Isabella in the telephone book, calls her, and leaves a message saying that Torey is looking for Chris and wants any information she has. After making the call Torey falls asleep, forgetting the call. Torey ignores his old friends and now ex-girlfriend at lunch; he and Ali sit with some "boons" instead. During lunch, the police, and Mrs. Creed, burst in to take Bo for questioning. Ali and Torey protest; both confess to the phone call, but the adults don't believe them and assume they are simply covering for Bo. In the principal's office, Torey attempts to explain to Mrs. Creed that Chris was socially awkward, but she still believes her son had "a very good life" and could not have wanted to kill himself or run away.
A few days later when Torey returns home from school he finds a message from Isabella on his answering machine telling him to "come over anytime" to talk about Chris. Ali and Torey then take a trip to Isabella's house and find out that she did not have a relationship with him but did have sex with him. Ali and Torey discover that Chris faked the whole relationship and wrote down the false information in his diary. Isabella also has Torey and Ali meet her psychic, Aunt Vera who proceeds to warn Torey that when he is alone he "will find him. In the woods."
Upon returning to the Adams' home, Ali and Torey decide to go to the woods to see if they can find Chris's body. They don't find him. When Torey gets home, he receives a call from his friend Alex, asking him to meet up. When they meet behind Torey's house, Alex indirectly accuses Torey of being an accessory to Chris Creed's alleged murder. When they finish arguing with each other, Torey ventures into the dark woods alone.
When Torey turns to return home, he sees an Indian Spirit, a memory from his childhood. Torey follows it, and ends up in an old Indian burial ground. He breaks his leg when a boulder falls on it, forcing him to crawl into a grave. He sees neatly wrapped bodies, but spots a human body that isn't like the others. When he gets closer, he immediately thinks it is Chris, though it's really Bob Haines. Suddenly, air rushes through the space where Torey had crawled in, and the corpse starts peeling apart. Torey is traumatized and is sent to a mental hospital to recover. Since he can't stand the Steepleton gossip, he finished his junior year of high school at home.
Torey realizes through the course of the story that truth changes with each person's perspective. Torey ends his narration of the novel by stating that Chris's body was never found, but he does show some hope, through letters from people he thought could be Chris in disguise.