Christopher John Francis Boone finds that Wellington, the poodle of his neighbor Mrs. Shears, has been killed. Christopher has difficulty reading people’s emotions, and he takes comfort in the predictability of prime numbers. He says he has written a murder mystery about Wellington’s murder. The police arrive and assume that Christopher is involved in the murder and take him to the police station until Father brings him home.
These chapters interweave Christopher’s recollection of his mother’s disappearance and death with the nascent stages of his investigation of Wellington’s murder, including his deduction that the murderer must have been acquainted with Mrs. Shears. We learn that Christopher finds comfort in logic, but more so in predictable order.
Christopher questions some of the neighbors and concludes that Wellington’s killer must have wanted to upset Mrs. Shears. Christopher recalls that Mrs. Shears helped his father after Mother’s death and that this was around the same time that Mr. Shears moved away. He decides that he needs to learn more about Mr. Shears.
Christopher explains his theories to Father, who gets angry at the mention of Mr. Shears’ name and tells him to abandon his murder investigation, which leads Christopher to retreat into his fantasy of becoming an astronaut. Christopher shows his now “finished” murder mystery to Siobhan, but it bothers him that the book doesn’t have a resolution.
Christopher encounters a neighbor, Mrs. Alexander, and decides he can talk about Mr. Shears since Father isn’t present. When Christopher asks if Mr. Shears killed Mother, Mrs. Alexander expresses shock in learning of Mother’s death, but assures him that Mr. Shears did not kill her, but rather had an affair with Mother.
Christopher expresses his admiration of Sherlock Holmes and The Hound of the Baskervilles, a murder mystery in which the highly observant Holmes sees through numerous misleading clues and solves a mystery involving a dog that is disguised to look like a horrifying supernatural creature. Siobhan wants to discuss Mother and Mr. Shears’ affair, but Christopher says he is not upset since Mother is dead.
Father becomes furious after learning that Christopher has found out about Mother’s affair and then hits him unconscious, although Christopher cannot recall if this for sure happened. Father tries to reconcile with him the next day.
Searching for his book hidden by Father, Christopher finds letters addressed to him from Mother and reads one, which confuses but also intrigues him, since it was apparently written after her supposed death.
By secretly reading the letters addressed to him, Christopher learns that Father deceived him into believing that Mother had died, but he also hears from Mother’s perspective about how difficult and stressful it was to raise him and how that led her to leave with “Roger.” Overwhelmed by these discoveries, Christopher passes out before awakening to Father crying.
When Father admits to Christopher that he lied about Mother and confesses that he killed Wellington, Christopher is horrified and decides he can no longer live with him. Christopher worries about the difficulty of traveling to London to find Mother, but after packing and taking Father’s money, he successfully deduces how to find the train station.
Although overwhelmed by unfamiliar surroundings, Christopher employs a series of mental exercises and manages to board the train for London. He is tracked down by a policeman who says he will take him back to Father when they reach the next station. However, Christopher evades the policeman and his journey to London resumes.
After a long, stressful day, Christopher arrives at the London apartment of Mother and Mr. Shears, where he describes his journey and explains Father’s deception before falling asleep. He awakes to the shouting of Father, Mother, and Mr. Shears, which is followed by the arrival of a policeman who escorts Father out after Christopher refuses any contact with him.
Christopher and Mother move to a cramped apartment near Father’s house as Mother struggles to cope with her upended life. Christopher takes his A-level math exam and gets a high score. Christopher adopts an optimistic view about his future, reasoning that although he knows it won’t be easy, he managed to solve the mystery of Wellington’s murder, find his mother, and write a book about it.