Fifteen-year-old Charlie is coping with the suicide of his friend, Michael. To lessen the fear and anxiety of starting high school alone, Charlie starts writing letters to a stranger, someone he heard was nice but has never met in person. (Kind of like when we write letters to Paul Rudd before we go to sleep.)

At school, Charlie finds a friend and mentor in his English teacher, Bill. He also overcomes his chronic shyness and approaches a classmate, Patrick, who, along with his step-sister Sam, become two of Charlie's BFFs.

During the course of the school year, Charlie has his first date and his first kiss, he deals with bullies, he experiments with drugs and drinking, and he makes friends, loses them, and gains them back. He creates his own soundtrack through a series of mix tapes full of iconic songs, reads a huge stack of classic books, and gets involved in the Rocky Horror Picture Show audience-participation culture.

Charlie has a relatively stable home life, though, with supportive, if distant, parents to fall back on. Unfortunately, a disturbing family secret that Charlie has repressed for his entire life surfaces at the end of the school year. Charlie has a severe mental breakdown and ends up hospitalized.

Charlie's final letter closes with feelings of hope: getting released from the hospital, forgiving his aunt Helen for what she did to him, finding new friends during sophomore year, and trying his best not to be a wallflower. Charlie hopes to get out of his head and into the real world, participating in life instead of just watching it fly by.