The story acts as a prequel to King's 1975 novel `Salem's Lot.
Charles Boone, in a series of letters addressed to an acquaintance nicknamed "Bones", describes the arrival of himself and his manservant, Calvin McCann, at Chapelwaite, the neglected ancestral home of Charles's estranged late cousin, Stephen. Stephen left the estate to Charles in an apparent gesture of good will, trying to repair an old rift between the two sides of the family. While running errands, Calvin finds that many people in the nearby town of Preacher's Corners, Maine think them mad for being willing to live in the mansion. The house is said to be "a bad house," with a history of sad events, disappearances, and mysterious noises which Charles attributes to "rats in the walls". Not long after their arrival, Calvin finds a hidden compartment in the library, containing an old map of a nearby deserted village called Jerusalem's Lot, a mysterious area the townsfolk avoid. Marked on the map is a church, with the label, "The worm that doth corrupt." Their curiosity piqued, Charles and Calvin set out to explore the remains of the town the next day.
They find the quaint Puritan settlement heavily weathered and decayed, but it is clear that no one has set foot in the town since its abandonment; not looters, collectors, children, nor animals, such as birds or spiders. The town, as described by Charles, is "sour". As Charles and Calvin explore the church described on the map, they discover an unspeakably obscene and sacrilegious Madonna and Child (Charles' 19th-century sensibilities prohibit any specific description) and an inverted cross. At the pulpit they find a book filled with Latin and Druidic runes, entitled De Vermis Mysteriis, or "The Mysteries of the Worm." When Charles touches the book, the church shakes and the two men sense something gigantic moving in the ground beneath them. The evil of the place overcomes both men, and they quickly leave the town.
Later, in Preacher's Corners, Charles finds that he (like his relatives before him) is greatly feared and cursed by all, to the point of being chased away from one house with rocks and guns. Finally, Charles turns to the former cleaning lady of Chapelwaite for information about the connection of his home and Jerusalem's Lot. She cites numerous evil omens which have occurred since Charles' residence at Chapelwaite, such as gathering flocks of whip-poor-wills and a baby born without eyes. She further reveals that the family rift was caused when Robert Boone, Charles' grandfather, attempted to steal De Vermis Mysteriis from his brother Philip, presumably to destroy it. She explains that Philip was a minister who became heavily involved in the occult, so much so that "the mark of the beast was on him." On October 31, 1789, Philip Boone vanished along with the entire population of Jerusalem's Lot. Charles attempts to dismiss it all as superstition, but he is unable to forget what he saw in the church in the abandoned town.
One morning, while Charles is asleep, Calvin discovers a diary in the library, encrypted with a cipher. Before he can examine it further, Charles enters. Tired of the noises behind the walls, Charles asks Calvin to venture with him into the cellar to check for rats. Two days pass before Charles has recovered enough to describe what they found hidden behind the walls: the ancient, undead corpses of two of his relatives, Marcella and Randolph Boone. Marcella fell to her death in the cellar, possibly from the missing stair run that is described by Charles as they descend into the cellar. Randolph is said to have hanged himself in the cellar due to the grief from Marcella's death. Marcella and Randolph approch Charles and Calvin from the dark corner and are described to still have the rope burn around Randolph's neck and Marcella's neck to be at an un-natural angle. Charles instantly recognizes them as "nosferatu." The two men fled the cellar, and Calvin immediately barred the door to prevent any pursuit from the creatures.
Meanwhile, as Charles recovers, Calvin continues his search for clues. He eventually finds the key to the cipher. With it, he is able to interpret the diary and presents his findings to Charles. The diary contains a history of Jerusalems's Lot and a record of the events in 1789 leading up to its abandonment. It is revealed that the town was founded by one of Charles' distant ancestors, James Boon, who was the leader of a cult of witchcraft and inbreeding that had split from the Puritans. The journal goes on to explain how, many years later, Philip and Robert Boone later returned to the area after Chapelwaite was built, how Philip was taken in by the cult in Jerusalem's Lot, and how he acquired De Vermis Mysteriis at the behest of the ancient James Boon. Philip descended into madness, and plagues fell upon Preacher's Corners. Philip and Boon are said to have used the book to call forth some kind of supernatural force referred to by Philip as "The Worm". In his final entry, Robert curses the flocks of birds that have descended upon Chapelwaite. The diary ends there.
Charles feels compelled to return to Jerusalem's Lot. Calvin does his best to prevent it, but he eventually gives in and accompanies his master to the village. Returning to the church, they discover a horribly butchered lamb on the altar, lying on top of De Vermis Mysteriis. Charles moves the lamb and takes the book, intending to destroy it, but a congregation of evil undead entities begins to emerge, including those of James Boon and Charles' great-uncle, Philip. Charles becomes possessed and begins to chant, summoning forth The Worm with an ancient spell. Calvin knocks down Charles, which snaps him out of his possessed stupor. Charles then manages to set fire to the book. The gigantic Worm, heavily hinted to be a form or incarnation of the Cthulhu Mythos deity Shudde M'ell, lashes out from below, killing Calvin, and then disappears. Before Charles can recover Calvin's body, the undead James Boon emerges from the Worm's hole, forcing Charles to flee the Church once more. In his final letter to Bones, Charles announces his intention to commit suicide, thereby ending the Boone family line and its connection to the evil of Jerusalem's Lot.
The book concludes with an "editor's note" that attributes Charles' letters (as well as the death of Calvin McCann) to insanity, dismissing his claims of supernatural occurrences in Jerusalem's Lot. Finally, the editor notes that Charles was not, in fact, the last of his line; that a bastard relative still exists -- the editor himself, James Robert Boone. He has moved to Chapelwaite, hoping to clear the family name, and notes that Charles was right about one thing: "This place badly needs the services of an exterminator. There are some huge rats in the walls, by the sound." The note is dated October 2nd, the same date as Charles's first letter.
The story was adapted into a segment of the graphic novel The Secretary of Dreams, Volume 1.