Christopher Boone is a mathematically extremely smart autistic (Asperger's Syndrome) boy who one night discovers the dead body of Wellington, a dog of his neighbor Mrs. Shears. After a confusion with the police that gets him arrested, Christopher decides to solve the mystery of who killed Wellington despite his father's order that he stay out of other people's business. Christopher's mother died of a heart attack two years earlier, and he live with his father, Ed Boone.
Christopher decides to write about this mystery for an assignment at school; the book he writes is the one we read as the novel. He is also preparing for his A-level math exam, which has never happened at his school before. Regarding Wellington's death, Christopher investigates around the neighborhood and eventually finds out from Mrs. Alexander that his mother Judy had an affair with Roger Shears, Mrs. Shears' former husband. Ed got angry when he discovers Christopher's book: they get into a fight and he throws the book away.
Christopher wants his book back and searches for it; when he discovers it in his father's bedroom, he also finds letter that seem to be from his mother. With his father unaware, he reads several of the letters and realizes his mother isn't dead but is living in London with Roger Shears. She had run away with Mr. Shears two years ago, unable to care for Christopher any longer. Christopher's father had lied to him by telling him she was dead.
Ed apologizes to Christopher for this lie, then also tells his son that he was the one who killed Wellington. He did because of frustrated and anger against Mrs. Shears, with whom he thought a romantic relationship was possible. Christopher panics at this news, and his father's ability to kill Wellington with the possibility of being murdered himself. He hides behind the shed that night and decides to go to London to live with his mother. With some difficulty,...