Quills begins during the Reign of Terror, with the incarcerated Marquis de Sade (Geoffrey Rush) penning a story about the libidinous Mademoiselle Renare, an aristocrat who meets the preeminent sadist in her executioner.Several years later with the Marquis confined to the asylum at Charenton, overseen by the enlightened Abbé du Coulmier (Joaquin Phoenix). The Marquis has been publishing his work through laundress Madeleine "Maddy" LeClerc (Kate Winslet), who smuggles manuscripts through an anonymous horseman (Tom Ward) to a publisher. The Marquis' latest work, Justine, is published on the black market to great success. Napoleon (Ron Cook) orders all copies of the book burned and the author shot, but his advisor, Delbené (Patrick Malahide), tempers this contentious idea with one of his own: send traditionalist Doctor Royer-Collard (Michael Caine) to look in at Charenton and silence the Marquis.Dr. Royer-Collard arrives, informing the Abbé that the Marquis' "therapeutic writings" have been distributed for public consumption. Horrified, the Abbé rejects Royer-Collard's offers of several archaic "treatments" and asks to speak with the Marquis himself, who promptly swears obedience (winking at Madeleine through a peephole). Royer-Collard takes his leave for the time being and travels to the Panthemont Convent in Paris to retrieve his promised bride, the underage Simone (Amelia Warner). They are given a run-down chateau by the Emperor, with a handsome young architect, Prouix (Stephen Moyer) on hand for its renovation.The hasty marriage incites much gossip at the asylum, prompting the Marquis to write a farce to be performed at a public exhibition. The audacious play, titled "The Crimes of Love", is interrupted when the inmate Bouchon (British character actor Stephen Marcus) molests Madeleine off-stage, prompting her to hit him in the face with an iron. Royer-Collard shuts down the public theater and demands that the Abbé do more to control the Marquis. Infuriated, the Abbé confiscates the Marquis' quills and ink, prompting more subversive behavior, including a story written in wine on bedsheets and in blood on clothing. This results in further deprivation, eventually leaving the Marquis naked in an empty cell.While this is occurring at the asylum, Simone has been violently introduced to the adult world by her husband. She unrepentantly purchases a copy of the Marquis de Sade's Justine, seduces Prioux, and the young lovers run off together. She leaves behind a letter explaining her actions and her copy of Justine. Upon finding this, Dr. Royer-Collard seizes on the Marquis as the source of his troubles and embarks upon a quest for revenge.About to be sent away from Charenton for her role in assisting the Marquis, Madeleine begs a last story from him, which is to be relayed to her through the asylum patients. Bouchon, the inmate at the end of the relay, is excited by the story, breaks out of his cell, and kills Madeleine. The asylum is set afire by the pyromaniac Dauphin (George Yiasoumi) and the inmates break out of their cells.Madeleine's body is found by her blind mother in the laundry vat and Bouchon is captured and imprisoned inside an iron dummy. The Abbé blames the Marquis for Madeleine's death and prods him into a fury. The Marquis claims he had been with Madeleine in every way imaginable, only to be told she had died a virgin. The Abbé cuts out the Marquis' tongue as punishment for his involvement. In a later scene, the Abbe commits necrophilia with the corpse of Madeline in a dream. The Marquis' health declines severely, though perverse as ever, he decorates his oubliette with a story, using feces as ink. As the Abbé finishes reading the last rites, he offers the Marquis a crucifix to kiss, which he swallows and chokes on, thus committing suicide.A year later, the new Abbé du Maupas (Alex Avery) arrives at Charenton and is given the grand tour. The asylum has been converted into a printing press, with the inmates as its staff. The books being printed are the works of the Marquis de Sade. At the end of the tour, the new Abbé meets his predecessor, who resides in the Marquis' old cell. Yearning to write, he begs paper and a quill from the Abbé, who is herded off by Royer-Collard, now overseer of the asylum. However, the peephole opens, and Madeleine's mother thrusts paper, quill, and ink through. The Abbé begins to scribble furiously, with the Marquis providing the narration.