The Monk has two main plotlines. The first concerns the corruption and downfall of the monk Ambrosio, and his interactions with the demon-in-disguise Matilda and the virtuous maiden Antonia. The subplot follows the romance of Raymond and the nun Agnes. The novel switches between the stories at moments of high suspense. At various points, the novel also includes several extended anecdotes of characters with Gothic backstories who tell their tales.
Ambrosio, the monk
Ambrosio was left at an abbey in Madrid as an infant and is now a famously celebrated monk. A beautiful and virtuous young woman, Antonia, goes to hear one of his sermons, and meets Lorenzo, who falls in love with her.
Ambrosio's closest friend among the monks, Rosario, reveals that he is a woman named Matilda, who disguised herself to be near Ambrosio. While picking a rose for her, Ambrosio is bitten by a serpent and falls deathly ill. Matilda nurses him. When he recovers, Matilda reveals that she sucked the poison from Ambrosio's wound and is now dying herself. At the point of her death, Matilda begs him to make love to her, and he agrees reluctantly. After having sex with Ambrosio, Matilda performs a ritual in the cemetery which cures her of the poison. She and Ambrosio continue to be secret lovers, but Ambrosio grows tired of her.
Ambrosio meets Antonia and is immediately attracted to her. He begins visiting Antonia's mother regularly, hoping to seduce Antonia. In the meantime, Lorenzo has secured his family's blessing for his marriage with Antonia. Matilda tells Ambrosio she can help him gain Antonia's charms, the same way she was healed of the poison: witchcraft. Ambrosio is initially horrified, but agrees. Matilda and Ambrosio return to the cemetery, where Matilda calls up Lucifer, who appears young and handsome. He gives Matilda a magic myrtle bough, which will allow Ambrosio to open any door, as well as rape Antonia without her knowing. Ambrosio uses the magic bough to enter Antonia's bedroom. He is on the point of raping her when Antonia's mother arrives and confronts him. In panic, Ambrosio murders her and returns to the abbey, unsatisfied in his lust and horrified that he has now become a murderer.
Antonia, grief-stricken at the death of her mother, sees her mother's ghost. She faints and Ambrosio is called to help. Matilda helps Ambrosio acquire a concoction that will put Antonia in a deathlike coma. While attending to Antonia, Ambrosio administers the poison, and Antonia appears to die. He takes Antonia to the crypt beneath the convent, where, she awakens from her drugged sleep and Ambrosio rapes her. Afterward, he is as disgusted with Antonia as he was with Matilda, who arrives to warn him that the convent is burning down due to a riot (caused by the events of Raymond and Agnes's story). Antonia attempts to escape, and Ambrosio kills her.
Ambrosio and Matilda are brought before the Inquisition. Matilda confesses her guilt and is sentenced to death. Before she is executed, she sells her soul to the devil in exchange for her freedom and her life. Ambrosio insists upon his innocence and is tortured. He is visited by Matilda, who tells him to yield his soul to Satan. Ambrosio again proclaims his innocence, but when faced with torture, he admits to his sins of rape, murder, and sorcery and is condemned to burn. In despair, Ambrosio asks Lucifer to save his life, who tells him it will be at the cost of his soul. Ambrosio is reluctant to give up the hope of God's forgiveness, but Lucifer tells him that there is none. After much resistance, Ambrosio signs the contract. Lucifer transports him from his cell to the wilderness. Lucifer informs him that Antonia's mother, whom he murdered, was also his mother, making Antonia his sister, adding to his crimes the sin of incest. Ambrosio then learns that he accepted Lucifer's deal only moments before he was to be pardoned. Lucifer reveals that it has long been his plan to gain Ambrosio's soul, and Matilda was a demon helping him. Finally, Lucifer points out the loophole in the deal Ambrosio struck: Ambrosio only asked to get out of his cell. Lucifer carries Ambrosio into the sky and drops him onto rocks below. Ambrosio suffers for six days before dying alone and damned for eternity.
Raymond and Agnes
Lorenzo's sister, Agnes, is a nun at the nearby abbey who is romantically involved with Raymond, son of a Marquis. Ambrosio hears the confession of the nuns at Agnes's convent. When Agnes confesses that she is pregnant with Raymond's child, Ambrosio turns her over to the Prioress of her abbey for punishment.
Lorenzo confronts Raymond about his relationship with his sister Agnes. Raymond tells their long history. Raymond was travelling in Germany when he was nearly killed by bandits. He avoided being killed, and rescued a Baroness who was also travelling. Visiting the Baroness afterward, Raymond fell in love with her niece Agnes. However, the Baroness was in love with Raymond; when he refused her advances, she made arrangements to send Agnes to a convent. Raymond and Agnes made plans to elope before Agnes left her aunt's castle for the convent. Agnes planned to dress as the Bleeding Nun, a ghost who haunted the castle and exited its gates at midnight. Raymond accidentally eloped with the real ghost of the real Bleeding Nun. Exorcising the ghost of the Bleeding Nun required assistance from the Wandering Jew. When Raymond was free, he found Agnes in the convent. There he seduced Agnes. When she discovered that she was pregnant, she begged him to help her escape.
When Raymond finishes his story, Lorenzo agrees to help him elope with Agnes. He acquires a papal bull releasing Agnes from her vows as a nun so that she may marry Raymond. However, when he shows it to the Prioress, she tells Lorenzo that Agnes died several days before. Lorenzo does not believe it, but after two months, there is no other word concerning Agnes. Eventually, to try to find Agnes, Raymond's servant disguises himself as a beggar and goes to the convent, where Mother St. Ursula sneaks him a note that tells Raymond to have the cardinal arrest the Prioress for Agnes's murder.
During a procession honouring Saint Clare, the Prioress is arrested. Mother St. Ursula publicly describes Agnes's death at the hand of the sisters. When the procession crowd hears that the Prioress is a murderer, they turn into a rioting mob. They kill the Prioress, attack other nuns, and set the convent on fire. In the confusion, Lorenzo finds a group of nuns and a young woman named Virginia hiding in the crypt. Lorenzo discovers a passage leading down into a dungeon, where he finds Agnes, alive and holding the dead body of the baby she had given birth to while abandoned in the dungeon. With Virginia's help, Lorenzo rescues Agnes and the other nuns from the crypt.
Virginia visits Lorenzo as he is recovering from his grief and the two become closer. Agnes tells the story of her miserable experience in the dungeon. Agnes and Raymond are married, and the couple leaves Madrid for Raymond's castle, accompanied by Lorenzo and Virginia, who are also eventually married.
