Christopher Boone is a fifteen-year-old boy, who experiences the world around him differently than most people. He likes prime numbers (which is why the chapters of the book are only prime numbers), he doesn't like to be touched, and he doesn't understand facial expressions or jokes.

One day he finds his neighbor's dog dead in her yard. A garden fork has been run through the dog. The dog's owner, Mrs. Shears, sees Christopher holding the dog and thinks he has killed it, so she calls the police.

As the policeman tries to question Christopher, he mentally shuts down. The policeman thinks he is being uncooperative and grabs Christopher by the arm. Christopher hits him and is arrested for assaulting an officer. The officer takes him to the police station and puts him into a cell. Christopher likes being in the cell, because it is a perfect cube. Christopher is very good at math and science, because they are logical and the rest of the world is illogical to him. After being released to his father, Christopher decides he should find out who killed the dog.

Christopher's father is not happy with this decision and tells him to leave the situation alone. Siobhan, Christopher's teacher's aide, tells him he should write a book about the mysterious death of the dog.

To write his book, Christopher realizes he needs to overcome his fear of strangers. He does this so he can talk to the neighbors, to see if they have any knowledge of who killed the dog.

Two years before, Christopher's mother died of a heart attack. Christopher wasn't allowed to go to her funeral, but his father told him about his mother's death. After his mother died, Mrs. Shears started to visit Christopher's house and eventually she started to spend the night there. Christopher liked this, because she cooked and cleaned for him and his father. Mrs. Shears did this, because her husband left her at about the same time as Christopher's mother died.

Christopher tries to interview Mrs. Shears and look in her shed for the garden fork, which killed the dog. He finds the fork, but Mrs. Shears tells him to leave or she will call the police. She calls Christopher's father, who tells Christopher he must stop investigating the dog's death.

At school Christopher wants to take his A level maths test, which after some discussion the headmistress allows. Taking this test is unique at Christopher's school, because it is a school for students with special needs. Christopher is enrolled there because he has a behavioral problem.

One of the neighbors Christopher talks to, about the dog, is Mrs. Alexander. She, one day, sees Christopher in a shop and they talk a little, she is surprised to hear his mother is dead. Christopher also tells her his father will not allow Mr. Shears name to be spoken in their home. She explains to Christopher that his mother and Mr. Shears had had an affair and that is why his father doesn't like Mr. Shears. She also makes Christopher promise not to tell his father she told him about the affair.

Christopher writes about the affair in his novel, which his father finds in the kitchen. He becomes very upset and he and Christopher have a fight.

His father throws the book away after the fight. Christopher looks for the book and finds it in his father's closet in a box. He also finds a letter in the box, which is addressed to him. He is confused, because the letter is written to him by his mother, after she died.

He later returns to the box and finds it contains forty-three letters all written to him by his mother. It is then he realizes his mother is alive and living in London with Mr. Shears. The discovery that his father lied to him makes him physically ill. His father returns home that evening and learns Christopher has found out the truth.

In an effort to regain Christopher's trust, his father promises to never lie to him again. To show Christopher he will not lie again, he confesses he killed Mrs. Shears' dog. He killed the dog, because he was angry with Mrs. Shears, after she refused to live with him.

This news devastates Christopher and he reasons if his father can kill a dog, then he could kill him. He feels the only safe course of action is to run away to live with his mother. He hatches a plan to take a train to London. His father is looking for him, with the help of the police, but Christopher manages to evade them.

The trip is frightening for Christopher, but he manages to find his way to his mother's apartment. His mother is glad to see him, but her boyfriend, Mr. Shears, is not happy to have Christopher living with them. Eventually the fighting between the Christopher's mother and Mr. Shears, along with his treatment of Christopher, causes her to take Christopher back to his home in Swindon.

There Christopher's father tries to gain Christopher's trust again, but Christopher is frightened of him. Christopher and his mother stay at the house, until she finds a job and moves them into a boarding house. Siobhan arranges for Christopher to take his A level maths test, which is very important to him. He receives an A on the test and he dreams of going to college.

Christopher slowly regains his trust in his father and they begin to rebuild their relationship. Christopher is happy, because he solved the mystery of the dead dog, received an A on his test, and found his mother.

This novel gives the reader insight into the world of a person with a behavioral problem. It also shows, that no matter what a person's unique abilities and challenges are, they can attain their dreams. Christopher is a unique young man who achieves his goals, while navigating the world on his own terms.