Christopher Boone is trying to discover who killed Mrs. Shear's dog, Wellington. He also talks about his life and how it affects his ability to conduct his investigation.

His life changed dramatically two years before the dog's death, after his mother died of a heart attack. Christopher was not allowed to see her, while she was in the hospital, prior to the heart attack, nor was he allowed to attend her funeral.

His mother's death changed the routine of his life, which is difficult for Christopher, because he doesn't adapt to change easily. He also has difficulty understanding directions, for instance, if a sign tells him to keep off the grass, then he wonders if this means just the grass around the sign or it means all grass. He needs directions spelled out in detail for him, which is what Siobhan, who helps him at school, does for him.

Christopher also has a hard time adjusting to new people. If the school hires a new teacher, he watches them for several weeks before he speaks to them, then he asks them questions about themselves. Only after going through these steps, does he feel comfortable being in the same room with them.

He starts his investigation into the dog's death by talking to Mrs. Shears, the dog's owner. She doesn't want to talk to him about the dog, so he sneaks into her backyard to look into her garden shed. He is trying to see if the garden fork, which killed the dog, is in the shed. He does see the fork, but he is caught looking in the shed by Mrs. Shears, who threatens to call the police if he doesn't leave.

The next day is Saturday and Christopher decides to try to overcome his dislike of strangers so he can question the neighbors, to see if they saw or heard anything on the Thursday night Wellington was killed. His inquiries are met with mixed reactions. Some of the neighbors have no idea what Christopher is talking about, while others tell him he should not question people about the dog. One older lady, Mrs. Alexander, who lives next door to Mrs. Shears, tries to befriend Christopher by offering him tea and biscuits. She, in his estimation, is gone inside the house too long, while she is making the tea, and so he leaves. His investigation of the neighbors yields no evidence he can use to discover the culprit behind Wellington's death.

Christopher begins to look at the case of the dead dog from a different point of view. He decides to use reasoning to find the killer. He starts wondering why a person would kill the dog and tries to discover who would be the most logical person to kill him. He reasons the killer is angry with Mrs. Shears and killed the dog to upset her. Mr. Shears left Mrs. Shears about two years ago and he did this because he didn't like her anymore. Christopher, therefore, reasons the person most likely to kill Wellington is Mr. Shears.

Christopher likes Mrs. Shears, because after his mother died, she would come to his house and cook for him and his father. Then she started to stay overnight at Christopher's house, when she did this she would clean up the house. This made Christopher happy, because he likes things neat and orderly. Because of his fondness for Mrs. Shears and his desire to find out who killed Wellington, Christopher decides to find out more about Mr. Shears.

Christopher goes to a school for children with special needs, but he thinks all the other children there are stupid. Christopher wants to take his A levels maths test, but the headmistress doesn't want him to take the test. His father argues with the headmistress and he finally convinces her to allow Christopher to take the test. No one at his school has ever taken A levels before, but Christopher is gifted in maths. The headmistress doesn't want Christopher to take the test, because the school is not set up to give the test. Father tells her he will pay someone to give Christopher the test after school and she finally agrees to the plan. Christopher has hopes of going to university and someday getting a job using his degree in maths and physics. He even hopes to marry one day, so he can have someone to take care of him and be his companion.

Christopher explains he has Behavioral Problems, which is why he is at the special school. These problems caused tension between his parents and they fought a lot. Some of his behavioral problems are not talking to people for long periods of time, not liking to be touched, and smashing things when he is angry or confused, but he is getting better as he matures.

That Saturday evening Father tells Christopher Mrs. Shears called him and told him about Christopher's snooping around her garden. He makes Christopher promise to stop investigating the death of the dog. Father also becomes enraged, after Christopher tells him he thinks Mr. Shears killed Wellington. He doesn't want to hear Mr. Shears name ever again, but he doesn't tell Christopher why.

Christopher explains to Siobhan his promise and says his book is complete. He doesn't like ending the book without finding out who the killer is, but Siobhan tells him sometimes in life the bad guy is not caught.

The next two days Christopher sees four yellow cars on his way to school, which means it is a Black Day. He sits alone, not speaking on those days, but the third day he closes his eyes on the way to school, so he doesn't have a third Black Day.

Christopher tries to find out who killed Wellington, but eventually his father makes him stop his investigation. We also find out that Christopher is very intelligent, despite having behavioral problems and he aspires to attend college, get a job, and get married.