The story starts in a family’s house, where the antagonist a man named Jack, murders everyone except the protagonist who is a toddler at the beginning. This toddler crawls out of his crib and to a nearby graveyard. After a long conversation among the graveyard residents, it is decided that the toddler can stay there, which is also the reason why he is saved from the man named Jack. The toddler is adopted by two ghosts, Mr. and Mrs. Owens; also the Vampire Silas takes care of him as a guardian. His parents give him the name Nobody Owens.
There are several stories of initiation integrated in this book. The first journey Bod takes is to the mausoleum in the graveyard with Scarlett. They both find a treasure which is guarded by a three-headed snake called “The Sleer”, and ancient tribe member called “The Indigo Man”. In this episode he manages to escape and save himself and Scarlett from the threat.
Also he is trapped one time by Ghouls in their city. By calling out the night-gaunts, he is able to flee from the danger. Afterwards, he realizes how important it is to listen to his teachers and follow their rules. Through his quest, of finding a headstone for the witch Liza Hempstock, Bod understands the importance of friendship. Also he realizes that a community can only exist if their members help and look after each other.
The graveyard residents decide that Bod should spend some time with the living as well. So he goes to school where he is not really one of the popular children. After a physical altercation with another boy, Bod decides to leave school and goes back to the graveyard. He meets Silas who tells him what has happened to his family and that the murderer of his parents is also looking for Bod to murder him.
Scarlett comes back with her mom to West Sussex because her parents have decided to get a divorce. Jack Frost, under the pseudonym Jay Frost, offers Scarlett a ride back home, so he can meet Bod through her. In a dream, Scarlett remembers Bod and the graveyard, so she goes there and looks for him. When they have found each other, Bod explains that he wants to find the murderer of his parents. Scarlett wants to help him and asks Jay Frost for help.
Scarlett sets up a meeting between Bod and Jay Frost. At this meeting the latter reveals himself as Jack Frost, the murderer of his parents. Now the story has reached its climax. Jack pulls out a knife and tries to kill Bod, but fails in his attempt. Scarlett and Bod run toward the graveyard to save themselves from the men. Bod encounters several members of the organization “The Jacks of all Trades”. One of them tells him the story about the murder of his parents and also that Bod was supposed to be murdered. They also tell him that Scarlett is being hunted by Jack Frost. Therefore, he runs to the mausoleum and sees Scarlett with a knife at her throat. With the help of the Sleer, Bod manages to kill Jack Frost and save Scarlett. Scarlett feels sorry for Jack Frost and gets angry at Bod for his inhumane actions.
Afterwards Silas takes Scarlett back to her mother where he erases all the information about Bod and the graveyard in Scarlett’s head. Bod is sent off by Silas to the real world, since there is no threat of being killed by the Jacks anymore. With a passport and some money he says goodbye to Silas and his parents Mr. and Mrs. Owens and steps outside in the real world.