Christopher John Francis Boone is a 15-year-old boy living in Swindon, England, with his widowed father, Ed. Christopher's mother, Judy, died from a heart attack two years prior to the events of the story. One night, Christopher discovers that his neighbour Mrs. Shears's dog, Wellington, has been fatally speared with a garden fork. As Christopher mourns over Wellington's body, Mrs. Shears calls the police. When a policeman grabs Christopher's arm, Christopher panics and hits him, so he is arrested for assaulting a police officer, though he is quickly released with a police caution. He decides to investigate the dog's death, chronicling any information he receives in a book. During his investigation, he meets the elderly Mrs. Alexander, who informs Christopher that his mother had an affair with Mr. Shears.
Ed discovers the book and confiscates it. While searching his father's room for the book, Christopher finds letters from his mother dated after her supposed death, leading him to become distressed and enter a catatonic state. Realizing that Christopher has discovered the letters, Ed admits to lying about Judy's death and reveals she is still alive and living in London with Mr. Shears. Ed also confesses that he had killed Wellington in anger after an argument with Mrs. Shears. Christopher decides to run away and live with his mother.
After a long, event-filled journey, evading policemen and feeling ill from the trains and crowds around him, he finally finds his way to the home of his mother and Mr. Shears, much to the delight of the former and chagrin of the latter. Soon after arriving, Christopher wants to return to Swindon in order to take his mathematics A-level. Judy leaves Mr. Shears as he becomes increasingly hostile towards both her and Christopher.
After an argument, Judy agrees to let Ed see Christopher for brief daily visits. Christopher remains apprehensive of his father, wondering if he will be imprisoned for killing Wellington. Ed gifts Christopher a puppy, promising that he will gradually rebuild trust with his son. Christopher declares that he will take further exams and attend university. He completes his mathematics A-level with top grades. The book ends with Christopher optimistic about his future.
