Philip Malloy is a track-obsessed ninth grader at Harrison High School in New Hampshire. After receiving a D on his English test, Philip blames it on his English teacher, Ms. Narwin. Since he is no longer eligible to try out for the track team, he avoids telling his parents and instead pretends that he no longer has an interest in trying out. Throughout his time in school, his number of class time disturbances increases.

One day, he begins humming the national anthem rather than maintaining respectful silence. Ms. Narwin asks him to stop multiple times. After three days of this behavior, he is suspended and given the chance to apologize to Ms. Narwin for his disrespect towards her. After Philip refuses, Vice Principal Dr. Palleni is called by district mandated procedure to suspend him. Philip tells his parents that he was suspended for 'singing' the National Anthem. Philip's father, Mr. Malloy, shares this with their neighbor, Ted Griffen, who is running for the school board. He arranges an interview between Philip and local journalist Ms. Stewart. Ms. Stewart investigates Philip's suspension story and ultimately publishes a newspaper article depicting the school's actions in an unpatriotic light.

Ms. Stewart's slanted newspaper article quickly garners national attention when it is picked up by the Associated Press, leading many to laud Philip for his patriotism and condemn the school's (alleged) attempts to stymie it. A reporter attempts to cover Ms. Narwin's side of the story, but her article is buried during an international crisis. In the midst of the controversy, Ms. Narwin is asked to 'take a break from teaching,' and she reluctantly agrees. This is soon followed by her resignation.

Meanwhile, Harrison School District faces a critical school board election bearing significant implications over the school's finances. With funding already in shortage, there is an urgent concern that the school could suffer greatly from further budget cuts. After using Philip's story as a platform, Ted Griffen is elected to the Harrison School District board. However, he declines to extend much-needed funding to Harrison High School in a demonstration of disapproval for their handling of Philip's incident.

When Philip returns to school, he has trouble adjusting to his dubious notoriety and becomes an outcast. His peers resent him for his role in the dismissal of Ms. Narwin and his invitation of a media firestorm on the Harrison community. He is harassed by other students both on the bus and in the classroom while his crush, Allison, openly resents him for the removal of her favorite teacher, Ms. Narwin. Philip is soon informed by a friend that the student body has begun drafting a petition with the intention to compel him into revealing the truth about the incident (an idea that originated from the track coach, Coach Jamison). This propels Philip into a breaking point and he begins skipping school, causing concern from his parents.

Philip ultimately decides to transfer to a private school, Washington Academy, despite protests from his father, as the tuition would use up all of his college funds and savings. The book ends in an incident at Philip's new school, where he is asked to lead his classmates in singing "The National Anthem". He cries and admits that he does not know the words.