[1] The novel begins with a prologue in the voice of an old man, Charles de Cresseron, that is set in Chapelizod, Ireland, roughly a century after the events of the novel proper.

This prologue details how, during an interment at the churchyard of the title, a skull is accidentally unearthed, which bears the marks of two crushing blows to the head and – even more disconcertingly – a small hole from a trepanning.

The novel itself is Cresseron's reconstruction of the history related to this grisly item (though by and large his narratorial voice drops out and the novel is told from a conventional omniscient narrator's point of view).

The first chapter of the novel proper moves back to 1767, the period of the novel, and begins with another mysterious occurrence in the churchyard: the secretive burial of a coffin, with the occupant simply identified on the brass plaque as "R.D."

The opening section of the novel is largely taken up by a farcical duel between two soldiers, Puddock and O'Flaherty, which arises from drunken misunderstanding and eventually is defused without any harm done.

Le Fanu introduces hints of unease, though, with the advent of the mysterious Mr Mervyn, who takes up residence in the Tiled House, a building widely rumoured to be haunted.

Sturk is troubled by vague recollections about Dangerfield, and gradually realizes that he is in fact the wily and dangerous Charles Archer, who actually committed the murder of Beauclerc.

Nutter disappears (after anonymously reporting the crime) and for a long time is assumed to have committed suicide, especially after a body is pulled from the river; but he is eventually discovered and put in jail, pending trial for the attack on Sturk.