When a sinister assassin attempts to murder a family of four, the family’s young toddler escapes to the nearby graveyard. After his mother’s spirit pleads for help, the ghosts agree to raise the toddler and protect him from the deadly threat. The elderly Owens ghosts adopt him and raise him as Nobody Owens. A mysterious being named Silas acts as his guardian and a link between the worlds of the living and the dead.
Although the dead acknowledge that Bod is a living boy and want him to have a full life, it is unsafe for him to leave the graveyard. Because the sinister man still seeks to kill him, Bod’s freedom is limited and he is unable to fully experience life.
Bod grows up with the Freedom of the Graveyard, allowing him to share many of the abilities of the dead. He learns lessons and makes friends with the ghosts around him. As he ages, however, he longs to know more about the living world and begins to test his boundaries by leaving the graveyard, going to school, and making friends with a living girl named Scarlett.
The assassin and his cronies, the Jacks of All Trade, chase Bod and Scarlett into the graveyard. One by one, Bod outwits them and uses his privileges of the graveyard to trap them. In a final showdown, he tricks Jack Frost in the barrow beneath the Frobisher mausoleum so that the Sleer drag him away forever.
Now that the Jacks are eliminated, Bod is safe. Silas permits Bod to leave the graveyard with him and continues to guide and support him for one more year in the graveyard.
At fifteen, Bod is fully grown and loses his Freedom of the Graveyard. He says goodbye to his family and friends and heads off to begin life in the land of the living.