The novel opens with the young narrator, Christopher John Francis Boone, discovering his neighbor’s dog dead in her yard, murdered with a pitchfork. Mrs. Shears, the neighbor who owns the dog, calls the police. When they arrive, they overwhelm Christopher with their questions, and when a policeman touches him roughly, Christopher responds by hitting him. The policeman arrests him and brings him to the station. Christopher makes it clear to his reader that he experiences the world differently than other people, and doesn’t understand human interaction very well.
At the police station, Christopher is put in a cell. The police call his father, Ed, who arrives angry at the police, but not at Christopher. An inspector questions Christopher and gives him a caution, which means that he’ll receive a punishment if he gets into trouble again. On the drive home, Christopher decides that he’s going to figure out who killed the dog, Wellington. Ed gets angry and tells him not to pursue Wellington’s death. Later that night, Christopher finds his father crying in the kitchen.
The next day, Christopher’s teacher, Siobhan, has him write a story, so he begins to write the story that becomes the novel. Although his father has told him to stay out of other people’s business, Christopher decides to disobey because Ed’s instructions are too vague. That evening, he goes to Mrs. Shears’s house and asks if she knows who killed Wellington, but she shuts the door in his face. He snoops in her garden shed and sees a pitchfork that looks like the one that killed Wellington.
The following day, Christopher decides to interrogate the other neighbors on his street, even though he doesn’t like talking to strangers. The first few people he talks to don’t have any information for him and advise him to discontinue his investigation. Finally, he approaches Mrs. Alexander, an older woman with a dog. She engages him in conversation and offers him refreshments, but when she goes inside to get them, Christopher decides she might actually be calling the police, so he leaves. He then reasons that Mr. Shears should be his prime suspect in the murder, because he left his wife, so he probably hated Mrs. Shears and killed Wellington in revenge. When Christopher returns home, Ed is very angry with him for continuing to investigate Wellington’s death, and he makes Christopher promise to stop.
In chapters alternating with those that cover the central action, the reader learns more about Christopher. He struggles to understand other people, but he loves math and science and is very good at them, so he plans to take the Maths A level exam to qualify for university. Furthermore, he always tells the truth, and he has a photographic memory. He hates brown and yellow, but he enjoys Sherlock Holmes stories, and models his own detective work on that of Holmes. His parents used to argue a lot, often about him. His mother, Judy, died two years earlier of an unexpected heart attack. After her death, Mrs. Shears helped his father out a lot around the house.
A few days later, Christopher runs into Mrs. Alexander at the corner store. She engages him in conversation, and he begins to ask questions about Mr. Shears. Eventually, Mrs. Alexander realizes that Christopher has illusions about his mother, and tells him gently that his mother was having an affair with Mr. Shears.
Christopher writes everything down in his book. A few days later, he accidentally leaves the book lying around, and his father reads it. He gets terribly angry with Christopher for continuing to snoop around, and when he grabs Christopher’s arm, the two get into a physical fight. Ed ends by throwing the book into the trash. The next day, Ed takes Christopher to the zoo in apology.
After school on the following day, Christopher searches the yard and the house for the book, in case Ed decided to take it out of the trash. He finally finds it in his father’s room, where he also discovers a number of envelopes addressed to him. He takes an envelope just as Ed gets home from work. When he reads it in private, he discovers that the letter is from his mother, but it was postmarked eighteen months after his mother supposedly died. Christopher sees this as another mystery to solve.
A few days later, Christopher returns to Ed’s bedroom and finds forty-three more letters addressed to him. He begins to read them. They’re full of his mother reminiscing about Christopher’s childhood and giving him updates about her life in London. In one, she explains that she left because she felt like she couldn’t be a good mother to Christopher, and she was in love with Mr. Shears. After a while, Christopher gets sick and blacks out. When he wakes up, his father comes in and realizes what has happened. Ed cries and apologizes for lying to Christopher, saying that he didn’t know how to deal with Judy leaving. He gives Christopher a bath, but Christopher won’t speak or eat.
Ed has learned that lying only causes more pain in the long run, so he decides to be brutally honest. He admits that he was the one who killed Wellington, because he was angry with Mrs. Shears for not wanting a relationship with him. Christopher becomes terrified of his father, thinking that if he killed Wellington, he might attack Christopher, too. Christopher waits until late at night, then sneaks outside and hides behind the garden shed. The next morning, Ed looks for him but doesn’t find him.
That morning, Christopher seeks help from Mrs. Shears and Mrs. Alexander, but eventually decides that he has to go to London to live with his mother, because he’s no longer safe with Ed. He takes Ed’s bank card and his own pet rat, Toby, and walks to school to ask Siobhan how to get to the train station. When he sees his father’s van in the school parking lot, he instead gets directions from a stranger on the street. He gets lost on the way to the station, but eventually finds it by walking the streets in a spiral.
The train station is very overwhelming for Christopher, but he makes it to a table at a café, where he sits and does mental math to stay calm. A couple hours later, he looks up to find a policeman asking what he’s doing there. The policeman helps him get money with Ed’s bank card, and directs him to the ticket office. Christopher purchases a ticket and finds his way to the train.
Just before the train leaves, the policeman shows up on board, this time with orders to bring Christopher back to his father. Before he can do so, however, the train begins to move. The policeman arranges for a car to pick them up at the next station. Christopher has to go to the bathroom, and then he hides on a luggage rack, because small spaces make him feel safe from the crowds on the train. The policeman can’t find him and leaves the train.
The train stops in London, and Christopher gets off. He’s overwhelmed by the number of signs in the station, but he finds his way to the information desk and asks how to get to his mother’s address. He’s directed to the London Underground, or the tube. In the tube station, he observes other people to figure out how everything works. He makes it to the platform of the train he needs to take, but when the train actually comes, he’s terrified by the noise. He sits on a bench for hours in a panic as the trains continue to roar in and out of the tunnel.
When Christopher’s fear lessens, he discovers that Toby has escaped. He sees him by the rails, and climbs down. A train comes just as he catches the rat, and a man on the platform has to pull Christopher to safety.
Finally, Christopher boards a train and gets off at his mother’s stop. He buys a street atlas from a shop in the station to find his way to his mother’s flat. When he gets there, Judy and Mr. Shears are shocked to see him. Christopher reveals that Ed told him Judy was dead, and that he never received her letters, which greatly distresses her. That night, Ed shows up in pursuit of Christopher. Christopher refuses to talk to him, and Mr. Shears calls a policeman to escort Ed out of the flat.
Life in London is not ideal for Christopher. His mother tries to take him shopping for clothes, but he can’t deal with the crowds. There’s no yard, and he can’t see the stars. When he remembers that he’s supposed to take his Maths A level the next week, Judy tells him he’ll have to wait until the next year. Furthermore, it’s clear that Mr. Shears doesn’t want him around.
When tensions with Mr. Shears heighten, Judy takes his car and drives Christopher back to Ed’s house. Ed is angry with Judy, but allows them to stay in the house temporarily while he lives with a friend. Christopher doesn’t eat or sleep, because he’s upset about not being able to take his A level. At school the next day, Siobhan and the school principal (Mrs. Gascoyne) decide he should still be able to take the exam, so he takes the first portion that very afternoon. He struggles because he hasn’t slept and can’t think properly. Over the next two days, he takes the rest of the exam, and feels better about it.
Meanwhile, Ed tries to get Christopher to forgive him, but Christopher is still scared of him. Judy finds a house of her own. Christopher lives with her, but he doesn’t like the house. He goes to Ed’s house for short periods of time, but still refuses to speak to him. Finally, he allows Ed to talk to him for just five minutes. Ed tells him that they need to make it a joint project to repair their relationship, and as a gesture of goodwill, he gives Christopher a golden retriever puppy. The dog, Sandy, lives at Ed’s house, where Christopher takes care of it and begins to interact with his father again.
Christopher receives an A on his exam, and he begins to study for the next A level. He plans to bring Sandy to university and become a scientist. He feels confident about his future because of all the challenges he has overcome in going to London and solving Wellington’s murder.