Still scared in the station, Christopher notices that Toby is missing. He looks for him and sees him on the tracks, so he jumps off the platform and follows Toby. A man on the platform tells him to get out but Christopher keeps trying to reach Toby and as he does, he hears the sound of the train. The man helps him on to the platform just in time.
Christopher boards the next train and gets off at Willesden Junction. He buys a map guide so that he can find Chapter Road, and when he gets to 451c Chapter Road his mother isn't in, so he waits. Christopher is cold and wet, and his mother runs a bath for him. His mother pleads with Christopher to allow her to just hold his hand, but he refuses. He tells her that his father said she was dead and that he never got any of her letters.
A policeman arrives and asks Christopher questions: had he run away and was this his mother? He answers yes, and when he tells them he wants to live with his mother, they leave. Christopher goes to sleep but wakes up at 2.31am and hears his father and mother and Roger shouting. After several angry words Christopher's father comes into Christopher's room and says he's sorry and holds out his right hand, spreading his fingers out in a fan with tears dripping off his face. But Christopher is frightened and doesn't meet fingers with him. Then a policeman takes Christopher's father out of the flat and Christopher goes back to sleep.
Christopher describes a recurring dream, in which a virus has killed most of the planet and the only survivors are those who prefer to stay away from other people, like him. This is a happy dream. With all the other people gone, Christopher can do what he pleases and explore the world without worrying about other people trying to talk to him or touch him.
The next day Christopher remembers that he has to go back to Swindon to sit his Maths A-level, but he doesn't want to see his father. His mother has lost her job as well. One night Mr Shears comes into Christopher's room and says 'You think you're so fucking clever, don't you? Don't you ever think about other people?'
The next morning Christopher and his mother pack the car and drive to Swindon. When they get to the house in Swidon, Christopher's parents argue, and his father goes to stay with a friend. The school arranges for the invigilator to come in so Christopher can sit his A-level, even though he is very tired. Soon Christopher's mother gets a job, and the two of them move into a room in a big house.
Christopher still won't talk to his father even though he has to stay in his house from 3.49 until his mother picks him up after work at 5.30. Christopher's father proposes that they do a project together, so he can show Christopher that he can be trusted. He reveals a golden retriever puppy - the puppy will be Christopher's if he goes to his father's house to walk it. Christopher begins spending more time at his father's and starts planning things for the future: to do further math A-level next year, then physics A-level the year after, then get a first class honors degree and then be a scientist. He knows he can do this because he solved the mystery, because he went to London on his own and because he wrote a book.
Losing Toby is the climax of the whole story. Although clearly Christopher will survive the jump on to the train tracks (as he is narrating the story), Haddon builds remarkable suspense. It is also notable that despite Christopher's difficulty connecting to other humans, he feels so strongly responsible for his pet rat that he will risk his life to find him. The key, of course, is that Christopher doesn't realize he is risking his life. His thinking is too compartmentalized - all he knows is that Toby is on the tracks, and therefore he should go on to the tracks to fetch him.
At the end of the novel Ed buys his son a puppy: there is renewal at the end of the novel where there was death at the start. Mr Shears shows himself to be as ignorant and insensitive as his previous wife and there is a symmetry to the whole story that must be pleasing to the narrator.
One of the most devastating moments in the novel is when Christopher refuses to let his mother hold his hand. She hasn't seen her son for two years, and he has just survived a truly terrifying voyage to reach her. And yet she cannot satisfy her maternal instinct to cuddle him. She cannot even hold his hand. Most people express their love through touch, but Christopher is incapable of this emotional experience, even as he understands it rationally. Therefore, those who truly love him, like his mother, are forced to work within his comfort range. And so the mother cannot hold her child. This moment vividly captures the difficulty of raising a differently-abled child.
The novel ends on a note of total happiness and hope. Not only has Christopher found his mother and normalized relations with his father, but he has also begun to learn to express his emotions in a way that is understandable by most people. He has written this book, which he knows is a huge accomplishment. But he also notes that his A level made him feel glad by drawing a smiley face - perhaps he doesn't smile himself, but he can identify his feeling with a facial expression. He has made progress.