When Bod is fourteen, Silas begins disappearing for long periods. Nobody knows where he goes, and the Owenses are upset when he leaves Bod behind without a guardian to provide food. While Silas is away, Scarlett Amber Perkins moves back to Bod’s town. She remembers little of her childhood there until one day she gets lost and finds the graveyard. She meets a nice man, Mr. Frost, who drives her home and befriends her mother. Slowly Scarlett remembers Bod again, and on another trip to the graveyard she spots him, seeing him even though he is Faded.

Although Bod is a little nervous around Scarlett, she is a welcome change from his ghost friends, who never grow older or change. He tells her about the murder of his family, and she studies the microfiche records at the library to find a report about the event. The murder took place in the house where Mr. Frost now lives, so she tells him about it, too. He is a historian, so he looks up the details and finds out that the murder was somehow hushed up. He tells Scarlett that one member of the family, a baby, belonged to the family and was never seen again after the event. When he learns all this, Bod realizes that he is at a crossroads in his life. Silas is not around to advise him, so he seeks the advice of the Sleer instead. The Sleer asks him to be its master. When Bod refuses, the Sleer encourages him to go after the murderer and find out his real name.

While Bod is learning about his history, Silas and Miss Lupescu are in Krakow with some allies. One dies in a magical spell involving mirrors. Later, a mysterious group of attackers pursues them. Miss Lupescu gets injured and cannot go on, so they all stand their ground and fight together.

Bod goes with Scarlett to speak with Mr. Frost, who tells them he has found a letter concerning the murdered family in the attic room of his house. He takes Bod into the room alone and pulls out a knife, revealing himself to be the man Jack who almost killed him fourteen years ago. Bod Fades and gets himself and Scarlett out of the house just as four men knock on the door. Before they leave, Scarlett learns that all the Jacks are Mr. Frost's friends.

Bod and Scarlett run back to the graveyard, where Bod hides Scarlett with the Sleer and turns to fight the Jacks. He tricks one man Jack into falling into a grave. He confronts three others by the ghoul-gate and learns from them that they are part of an organization, the Jacks of All Trades, that has been stealing magic from the dead for thousands of years. Once, in Ancient Egypt, a prophecy predicted that a boy would be born “who would walk the borderland between the living and the dead” and who would cause the end of the Jacks of All Trades. After learning this, Bod closes the ghoul-gate on them.

The last Jack, the one who killed Bod’s family, follows Scarlett to the Sleer’s lair. Bod follows them inside and confronts Jack, who takes Scarlett hostage. Bod shows Jack the Sleer’s treasure and tricks him into saying he wants to be the Sleer’s master. The master has to be dead, so the Sleer kills Jack. By now, Bod has figured out that Silas is systematically destroying the rest of the Jacks of All Trades, so Jack Frost is the last of them. When he is gone, Bod climbs back out of the barrow with Scarlett.

When she realizes that Bod knew what the Sleer might do, Scarlett is horrified. She accuses him of being a “monster” and using her as “bait.” Silas returns, having won his battle with the rest of the Jacks, and erases her memories of the events. Afterward, Bod says he wishes he could have remained friends with Scarlett, but Silas says it is better if she does not know what she cannot believe.

After everything that has happened, Bod would like to ignore life for a while. But like all living people, he gets hungry. Nobody is trying to kill him anymore, so Silas takes him out of the graveyard for pizza.