Even before her son Kevin was born, Eva Khatchadourian struggled with parenthood and a sense of ambivalence about becoming a mother. Owing to the fact that Kevin was a difficult infant and child, she gave up her successful career as a writer and publisher of travel guides in order to concentrate on raising him. Something has gone wrong, however, because her son has developed sinister psychopathic traits, though his father, Franklin Plaskett, refuses to acknowledge the problem. As the situation turns catastrophic, Eva tries to figure out where she and Franklin went wrong.
In the wake of a school massacre committed by the 15-year-old Kevin, Eva begins writing letters to Franklin in November 2000. She reflects candidly on the history of her relationship with her husband and the events of Kevin's life up to the killings. She also relates her current life: she was involved in both her son's criminal trial and a civil action against her (for parental negligence) brought by the mother of one of her son's victims. Eva sold the family home to pay for legal expenses, but in order to be near Claverack Juvenile Correctional Facility where Kevin is incarcerated, she still lives in the same town in which she remains shunned by the community. She regularly visits Kevin in prison, wherein they have a cold relationship.
Eva reluctantly stepped back from her career to raise Kevin, and the two have long been locked in a battle of wills. Kevin seemingly regards everyone, especially his mother, with contempt and hatred, yet pretends to be manageable when Franklin is around. Eva perceives him as deliberately antagonistic, with his behavior ranging from seemingly petty sabotage of Eva's belongings to possibly encouraging a girl to gouge out her eczema-affected skin. Kevin resisted toilet training, which Eva reveals led her to lash out and break Kevin's arm; Kevin told Franklin this was an accident and has since used the secret to manipulate Eva.
When Kevin is severely ill as a child, he briefly accepts Eva's care for the first time and rejects that of Franklin, seemingly too tired to put on an act of apathy. Eva reads Robin Hood to him, and he takes pleasure in learning archery after he recovers, yet he seems otherwise unable to relate to human passion. As he grows older, he also takes an interest in manipulating his sycophantic friend Leonard, engaging in vandalism, and collecting computer viruses on floppy disks. He unsettles his peers, expresses his disdain for convention by wearing uncomfortably undersized clothes, and follows news of school shooters and mass murderers. In high school, Kevin, Leonard, and two other boys accuse their drama teacher of sexual abuse; Eva is convinced he orchestrated the false accusations.
As Kevin's behavior worsens, Franklin defends him, convinced that his son is normal and instead just often misunderstood. Kevin plays the part of a loving, sensitive son whenever Franklin is around. Eva's apparent dislike for her son and the equally apparent distrust between Eva and Kevin, as well as the mounting distrust between Eva and Franklin, create a rift between the married couple. They have a second child, Celia, whom Franklin believes Eva favors. Kevin is often aggressive towards Celia and takes advantage of her affectionate nature. When Celia is six years old, her pet rodent disappears, and shortly after the sink in the children's bathroom becomes clogged, which Eva clears with a caustic drain cleaner. While Kevin is babysitting Celia, she supposedly finds the cleaner and accidentally destroys her eye and scars her face. Eva is certain that she put the cleaner away and Kevin attacked Celia with it. This accusation leads Franklin to ask for a divorce, intending to take custody of Kevin; Kevin overhears them.
When Eva relates the story of the massacre itself, it is finally revealed that Franklin and Celia are dead. Kevin had killed them both at home with his crossbow before going to his school, where he lured and trapped nine classmates, a cafeteria worker, and a teacher in a gymnasium and attacked them. Eva speculates that he did this because separation in the divorce would deny him a final victory over his mother, or to avoid being trapped in performing normalcy for Franklin. She also believes he selected the people he chose for his victims because he resented them for having interests about which they were passionate. Kevin ensured himself a light sentence by timing the attack for three days before his 16th birthday in order to be charged as a minor, and he used a prescription for Prozac to argue that he was experiencing violent psychotic episodes as a side effect.
The novel ends on the second anniversary of the massacre, shortly before Kevin will turn eighteen and be transferred to Sing Sing, a maximum security prison. Subdued and frightened, he gives Celia's prosthetic eye to Eva and apologizes. Eva asks Kevin for the first time why he committed the murders, and Kevin replies that he is no longer sure. They embrace, and Eva concludes that, despite what he did, she loves her son, and she awaits the day he is released so that she can welcome him home again.
