In Neil Gaiman's The Graveyeard Book, the primary setting of the story is the graveyard, where Bod ("Nobody") is raised after the murder of his family, and his unexpected escape.
Within the graveyard, there are places where Bod should not go: for instance, he enters the world of the ghouls and has to be saved by Miss Lupescu before the frightful creatures take his memory...and/or eat him. This worries his protector at the time, and Miss Lupescu faces dangers of her own in saving Bod.
When Bod visits the Indigo man, he meets an ancient race called the Sleer, who are dedicated to protecting the treasures within for their Master. While he goes where he should not, and the visit is at first fearsome, it will later help him, as will his experience with the ghouls. (It causes a great deal of concern on the part of Scarlet's parents—she is Bod's friend; with this incident the parents are sure Scarlet has been kidnapped).
Falling from a tree into unconsecrated ground, Bod meets a witch. While there is concern that she might be dangerous for Bod (on the part of members of the graveyard community), Liza Hempstock ends up helping Bod several times.
The most dangerous setting in the novel is outside of the graveyard—this causes Bod the most immediate, long-standing threat. At one point in order to make money, Bod tries to sell the Sleer's treasure. One man in a pawn shop knows the murderer of Bod's family—a man trying to find a missing boy about Bod's age, and almost captures Bod long enough to contact the murderer. While Bod escapes with Liza's help, it is clear that someone is still trying to kill him.
When Scarlet reappears and they go outside to visit Mr. Frost—who seems to have news of Bod's family—Frost turns out to be "Jack," the murderer who is trying to find him and "finish the job." By leaving the graveyard, Jack knows Bod is alive, he and his "cohorts" follow Scarlet and Bod back to the graveyard, and there is danger not only for Bod, but also for Scarlet who Jack also threatens.
These are the major scenes within the novel, each one bringing one kind of conflict with it or another.