Christopher John Francis Boone has found his neighbor's pet poodle lying on the ground with a garden fork stuck through him. The dog is dead and Christopher is upset at the sight of the dog, who he likes, so he picks up the dog to cradle him in his arms. Mrs. Shears, the dog's owner, and Christopher's neighbor, sees Christopher with the dog in his arms and thinks Christopher has killed the dog, so she calls the police.

Christopher is a fifteen-year-old boy, who looks at the world in a unique way. He is fascinated with prime numbers, which is why the chapter numbers of the novel are only prime numbers. He thinks prime numbers are like life, because "they are very logical but you could never work out the rules, even if you spent all your time thinking about them". He likes things to be logical and organized, he has difficulty discerning what facial expressions mean, and he hates to be touched. Christopher lives with his father, because his mother died two years ago.

When the police show up Christopher is relieved, because to him the police are logical. They have a purpose in the community and they wear uniforms; all of which calm Christopher. The policeman begins to ask Christopher questions about the dog's death, but to Christopher it is all too much. Having people talk to him too quickly or requiring him to answer questions in succession, causes Christopher to shut down. He explains the feeling by comparing his mind to a bread slicer at a bakery where "sometimes a slicer is not working fast enough but the bread keeps coming and there is a blockage". The words and questions causes his mind to have a blockage. The policeman, of course, doesn't know how Christopher's mind works and thinks he is being uncooperative. He reaches out to take hold of Christopher's arm and Christopher hits him, which results in him being arrested for assaulting a police officer.

Christopher enjoys the ride in the squad car, because he is able to see the stars through the window. Christopher loves anything having to do with math or science, because they have a logic and order to them, which makes him feel safe. He even enjoys being put in a cell, as the cell is a perfect cube. He also devises an escape plan, while he waits to see what will happen next.

His father arrives and manages to talk the police into releasing Christopher into his custody. The police detective explains to Christopher he will have a caution put in his record, to let the authorities know he has been in trouble before. Christopher understands what he is being told and then he returns home with his father.

Christopher, while at the police station, is asked several times if he is lying, when he denies killing the dog. He explains he is not lying, because he never lies, as he is incapable of telling a lie.

On the way home, he tells his father he is sorry he had to get him from the police station. His father is kind and tells him it is ok, but he also tells him he must keep out of trouble. Christopher agrees he will stay out of trouble and then he tells his father he is going to find out who killed the dog. His father becomes angry with Christopher, because he knows this could cause him to get into trouble again. Christopher's father tells him to leave the death of the dog alone, but Christopher can't leave it alone.

The next day on the way to school he sees four red cars in a row, which means it will be a Good Day. Christopher has a way of telling if a day is Good or Bad. If he sees four red cars in a row, then it is going to be a Good Day, three red cars a Quite Good Day, five red cars a Super Good Day and four yellow cars a Black Day, which is a day he doesn't speak to anyone. Because it is a Good Day, he decides he should try to find out who killed Wellington, the dog.

His teacher's aide, Siobhan, tells him the assignment that day is to write stories, so he should write about finding the dog and his trip to the police station. Christopher thinks this is a great idea and expands on the idea by deciding to write a mystery novel about finding Wellington's killer. Siobhan offers to help Christopher by correcting the grammar and spelling in his novel.

Siobhan has known Christopher for eight years and always tries to help him navigate the world around him. Since he has difficulty deciphering the meaning of facial expressions, she draws many different expressions on a piece of paper and writes what each expression means. This is somewhat helpful to Christopher, but people's expressions often change too quickly for him to find the correct one on the paper.

Christopher also has trouble with the usage of metaphors and jokes. He tries to form pictures in his mind of the metaphor, but they don't match what the person is trying to convey. Jokes are like many people trying to talk to him all at once, which overwhelms him. An example of this is a joke, which is a play on words, such as the joke his father tells, "His face was drawn but the curtains were real." The multiple meanings of the word drawn confuses Christopher.

Christopher is a teenager to whom the world is often a confusing place. He has difficulty if he feels he is being barraged with words and needs the logic of math, especially prime numbers, to calm him. He finds the neighbor's dog dead and decides to find who killed the dog, to make sense of the murder. To accomplish this goal, he tries to write a mystery novel about the dog's death.