The novel is a first-person narrative told from the point of view of the adolescent girl Maud Ruthyn, an heiress living with her sombre, reclusive father Austin Ruthyn in their mansion at Knowl. Through her father and her worldly, cheerful cousin, Lady Monica Knollys, she gradually learns more regarding her uncle, Silas Ruthyn, a black sheep of the family whom she has never met; once an infamous rake and gambler, he is now apparently a fervently reformed Christian. His reputation has been tainted by the suspicious suicide of a man to whom Silas owed an enormous gambling debt, which took place within a locked, apparently impenetrable room in Silas's mansion at Bartram-Haugh.
In the first part of the novel, Maud's father hires a French governess, Madame de la Rougierre, as a companion for her. Madame de la Rougierre terrifies Maud and appears to have designs on her; during two of their walks together, Maud is brought into suspicious contact with strangers that seem to be known to Madame de la Rougierre. (In a cutaway scene that breaks the first-person narrative, we learn that she is in league with Uncle Silas's good-for-nothing son Dudley.) The governess is eventually dismissed when she is discovered by Maud in the act of burgling her father's desk.
Maud is asked in obscure terms by her father if she is willing to undergo some kind of "ordeal" to clear the name of her uncle, and of the family more generally; shortly after she assents, he dies. At the reading of his will, it emerges that her father added a codicil to it: Maud is to stay with Uncle Silas until she comes of age; if she dies whilst still a minor, the estate will pass to Silas. Lady Knollys, together with Austin's executor and fellow Swedenborgian, Dr. Bryerly, attempt in vain to overturn the codicil, realizing its many dangerous implications for the young heiress; despite their efforts, Maud consents willingly to spending the next three and a half years at her uncle's mansion at Bartram-Haugh.
Maud initially finds life at Bartram-Haugh strange but not unpleasant, despite ominous signs such as the uniformly unfriendly servants and a malevolent factotum of Silas's, the one-legged Dickon Hawkes. Silas himself frightens Maud but is nonetheless seemingly kind to her, in contrast to his treatment of his own children, the loutish Dudley and the uneducated Millicent ('Milly'). Initially deprecating of her rustic mannerisms, Maud and Millicent become best friends, and each other's only source of companionship at the estate. During her stay, Maud is subject to various attempts by Dudley to court her, but she rejects him thoroughly on each occasion. Silas is periodically subject to mysterious catatonic fits, attributed to his massive opium consumption.
Various ominous happenings begin to take place at Bartram-Haugh; it becomes increasingly difficult for Maud and Millicent to find any route out of the estate; meanwhile, Dudley's courtship culminates in a marriage proposition to Maud; when she confronts Silas about it, he attempts to coax her into accepting. She is relieved when it emerges that Dudley is already married, and when, after being disowned by his father, he and his wife leave to set sail from Liverpool to New York. It is afterwards decided that Millicent should attend a boarding school in France, and Silas sends her away with the promise that Maud is to join her after three months.
In the meantime, Maud is shocked to discover Madame de la Rougierre residing at Bartram-Haugh in the employ of Silas, and she suspects also that Dudley may not have fled. Despite strong protest by Maud, Madame is charged with accompanying her first to London, and then on to Dover and across the Channel. After falling asleep during the journey and being escorted under the cover of darkness, Maud awakes to find herself again at Bartram-Haugh: she had in fact been on a round trip to London and back. Maud finds herself now imprisoned in one of the mansion's many bedrooms under the guard of Madame de la Rougierre, whilst everyone suspects she is in France. Remembering the earlier warnings of her cousin, Lady Knollys, she refuses to drink any of the drugged claret intended for her; instead, Madame de la Rougierre, ignorant of Silas' true intentions, partakes of it and promptly falls asleep on Maud's bed. Later that night, Dudley scales the building and enters the unlit room; the window he uses is set upon concealed hinges that allow it to be opened only from the outside. Hidden out of sight, Maud witnesses Dudley brutally murder Madame de la Rougierre by mistake in the near-darkness. Uncle Silas enters the room, having been waiting outside; as he does this, Maud slips out undetected. Assisted by Dickon Hawkes' daughter, whom Maud had befriended during her stay, she is swiftly conveyed by carriage to Lady Knolly's estate, and away from Bartram-Haugh.
Silas is discovered in the morning lying dead of an opium overdose, while Dudley becomes a fugitive and is thought to be hiding in Australia. Maud is happily married to the charming and handsome Lord Ilbury and ends her recollections on a philosophical note:
This world is a parable the habitation of symbols the phantoms of spiritual things immortal shown in material shape. May the blessed second-sight be mine to recognise under these beautiful forms of earth the angels who wear them; for I am sure we may walk with them if we will, and hear them speak!
Output: What finally claims the life of Uncle Silas?