In a small English village, a frightening-looking man named Jack prowls through a house. He’s already murdered the resident couple and their daughter; all that’s left is to murder their toddler son. The baby has no idea he’s in danger, but he is wily and adventurous and climbs out of his crib and out the front door. The baby then toddles up the hill toward the nearby graveyard. Once the baby is inside the gates, the ghost of Mrs. Owens envelops it in a hug. Her husband (Mr. Owens) and the graveyard’s other resident ghosts insist that they can’t get involved with a living child. But when the ghost of the baby’s mother appears, she points out Jack and begs the other ghosts to protect her child. The ghosts debate all night whether or not to keep the toddler, but they decide he can stay. The Owenses name the child Nobody Owens—“Bod” for short—and they give him the Freedom of the Graveyard, which allows him to see and interact with the dead and also grants him some ghostly abilities like walking through walls within the graveyard. Mr. and Mrs. Owens become Bod’s adoptive parents, while Silas, a vampire, becomes Bod’s guardian since he can pass for human and fetch food from outside the graveyard.
When Bod is four, he becomes friends with a little girl named Scarlett and the two play in the graveyard together. Eventually, the children learn that the oldest resident of the graveyard is buried in an underground barrow grave. When they explore the barrow, it’s not scary or particularly interesting. A slithering creature called the Sleer guards a few treasures for its master, who is gone. Not long after this, Scarlett moves away.
Silas introduces Bod to Miss Lupescu, who will be his temporary guardian while Silas is away for a month. Bod hates her immediately. She feeds him strange food and teaches him by giving him lists to memorize. Fed up with her boring lessons and feeling frustrated, Bod sits down on an ugly, water-stained grave to brood. Three ghouls find Bod there, listen to his tale of woe, and offer to take him to a city called Ghûlheim. They open the grave—a ghoul-gate—and toss Bod through. Bod knows he’s made a huge mistake. But thanks to Miss Lupescu’s lessons, Bod remember how to call for help in the language of the night-gaunts, giant birds that inhabit Hell. While Bod is traveling against his will with the ghouls to the hellish city of Ghûlheim, a wolf attacks the ghouls. To Bod’s surprise, it’s Miss Lupescu—the night-gaunts alerted her to Bod’s predicament. After this, Bod loves her, and she returns every summer to teach him.
When Bod is 10, he hears about a witch who was supposedly buried in the graveyard. His adoptive parents won’t tell him anything about her, while other ghosts suggest that the witch and other criminals were buried in Potter’s Fields, not the actual graveyard, and are bad people. But when Bod encounters the witch, Liza Hempstock, he’s surprised that she’s a young teen, not an ugly hag. As they talk, Liza admits that she’s still upset that she was disrespectfully buried without a headstone. Determined to fix this, Bod goes to the barrow grave and decides to sell one of the treasures, a brooch, to an antiques dealer and use the money to purchase a headstone for Liza.
The dealer, Abanazer Bolger, a selfish, greedy man, immediately knows the brooch is special. He locks Bod in his office and calls his associate, Tom Hustings. As Abanazer and Tom discuss the brooch and whether to call a man named Jack about the boy, Liza finds Bod in the office. (Unlike other ghosts in the novel, she wasn’t buried in the actual graveyard and thus isn’t confined there.) She helps Bod retrieve the brooch and escape. Bod makes Liza a headstone out of a glass paperweight, which she appreciates
That winter, funny things start to happen. Bod’s ghost friends start reciting rhymes about a “Macabray” and white flowers suddenly bloom in the graveyard. Later, when Bod can’t find anyone in the graveyard, he follows the sound of music to the town square. There, he watches the ghosts leave the graveyard and come down to dance the Macabray with the living. Bod dances with Liza and the Lady on the Grey. The next day, nobody will talk to Bod about what happened.
Around the same time, Jack attends a special dinner with about 100 other men. A man called Mr. Dandy reminds Jack that it’s important to finish what he started years ago and kill the boy.
As Bod gets older, Silas tells Bod about how he came to the graveyard and that Jack still wants to murder him. Bod insists on going to school so that he learn everything he can; Silas grudgingly agrees. Things go well for a few weeks, and Bod goes through his days partially invisible (one of his ghostly skills). But when Bod realizes that two kids, Nick and Mo, are bullying younger students, he knows he has to intervene. Using his ghostly abilities, Bod attempts to scare Nick and Mo into abandoning their bullying tactics, and though Bod is able to frighten Nick into reforming, Mo is set on revenge. Eventually, Bod and Silas agree that it’s too risky for Bod to continue going to school. Silas does allow Bod to return to school once more to frighten Mo, though.
When Scarlett is 15, her parents divorce. She and her mother return to Bod’s village. The bus system is difficult to navigate and one afternoon, Scarlett unintentionally ends up in the graveyard where she played as a child. There, she meets a friendly historian, Mr. Frost. He drives her home and strikes up a friendship with Scarlett’s mother. Scarlett reconnects with Bod in a dream and visits him in the graveyard soon after. They discuss the murder of Bod’s biological family, and Scarlett throws herself into researching the crime. With Mr. Frost’s help, Scarlett discovers that the authorities never solved the case—and that Mr. Frost lives in the house where Bod’s family once lived. When Mr. Frost uncovers new information about the murder and offers for Bod to come over and talk, Bod is unsure if he should leave the graveyard. Silas is gone, so Bod asks the Sleer for advice, but it just cryptically tells Bod to learn his name. Bod goes to Mr. Frost’s house with Scarlett, hoping to find out the name he was given at birth. But there, Bod is horrified to learn that Mr. Frost is actually Jack.
Several of Jack’s colleagues arrive in the village to help Jack track down Bod. Meanwhile, Bod and Scarlett run out of Jack’s house and flee to the graveyard. Bod hides Scarlett in the barrow grave, and then sets about dealing with Jack and his cronies. Silas and Miss Lupescu are still abroad, so Bod has to fight alone. Mr. Dandy explains that they want to murder Bod because of a prophecy that says a boy (whom they think is Bod) will bring about the end of their organization, the Jacks of All Trades. Bod tricks Mr. Dandy and several of his men into fall through the ghoul-gate, and Bod tricks another into falling into a deep grave, where he breaks his ankle.
Meanwhile, Jack pursues Scarlett into the barrow grave. Jack seems not to care that he’s the last Jack of All Trades—Bod has defeated all the others—and when he notices the Sleer’s treasures, he decides to start a new organization that will begin with Bod’s murder. Though Bod initially wants Jack to tell him what his birth name was, Bod realizes it doesn’t matter—he’s Nobody Owens. Thinking quickly, Bod encourages the Sleer to talk about its desire to find a new master, and Jack accepts the role, believing this will make him all-powerful. Instead, the Sleer winds around Jack with its snakelike body and imprisons Jack in the walls of the barrow. Scarlett, disturbed and frightened, accuses Bod of being a monster. Silas returns to the graveyard just in time to erase Scarlett’s memory and convince Scarlett’s mother to move back to Glasgow. Silas also finally explains to Bod that he and the Honour Guard have been pursuing the Jacks for years and that Miss Lupescu died to protect Bod.
About a year later, Bod struggles more and more to see the ghosts. It’s hard or impossible to slip through walls, too. One night, Silas offers Bod a suitcase containing money and a passport—it’s time for Bod to enter the real world. Bod solemnly shakes Silas’s hand and walks to the gates of the graveyard. There, Mrs. Owens is waiting. She sings Bod a lullaby and disappears when Bod tries to hug her. Bod leaves the graveyard, excited for his future.
