Quills opens amidst the chaos of the Reign of Terror, where the imprisoned Marquis de Sade (played by Geoffrey Rush) is deeply engrossed in crafting a provocative narrative about the debauched Mademoiselle Renare. This aristocrat finds herself entangled with her sadistic executioner. Fast forward several years, the Marquis finds himself confined within the walls of the Charenton asylum, under the watchful eye of the enlightened Abbé du Coulmier (portrayed by Joaquin Phoenix). Here, the Marquis cleverly disseminates his writings through the laundress, Madeleine "Maddy" LeClerc (played by Kate Winslet), who covertly transmits his manuscripts, using a mysterious horseman as her courier to reach the publisher.
The Marquis's latest literary endeavor, Justine, gains notoriety on the black market. Infuriated by the burgeoning success, Napoleon (Ron Cook) demands the destruction of the book and calls for the Marquis's execution. However, his advisor, Delbené (Patrick Malahide), introduces an alternative plan: send the traditionalist Doctor Royer-Collard (portrayed by Michael Caine) to silence the Marquis once and for all.
Upon his arrival, Dr. Royer-Collard informs the Abbé that the Marquis’s so-called "therapeutic writings" have reached the public, leaving the Abbé horrified. Rejecting Royer-Collard’s archaic methods of treatment, the Abbé seeks out the Marquis, who playfully swears obedience while sneaking a flirty glance at Maddy through a peephole. Dr. Royer-Collard soon departs to secure his promised bride, the underage Simone (Amelia Warner), yet the commotion within the asylum prompts the Marquis to write a farcical play, The Crimes of Love. The chaotic atmosphere escalates when an inmate, Bouchon (Stephen Marcus), attempts to assault Maddy during the performance, leading to a violent confrontation.
Dr. Royer-Collard, incensed by this incident, orders the closure of the public theater and insists on a firmer control over the Marquis. As tensions rise, the Abbé retaliates by seizing the Marquis's quills and ink, igniting a series of rebellious acts from the Marquis—he starts composing stories on bedsheets with wine and on clothing with his own blood. The cruel punishments ultimately leave him isolated and stripped of dignity.
Meanwhile, Simone becomes embroiled in tumultuous adult experiences with her husband. Defiantly, she buys a copy of Justine, begins an affair with the architect Prouix (Stephen Moyer), and the pair abscond together, leaving a letter and her copy of Justine behind. This betrayal leads Dr. Royer-Collard to view the Marquis as the root of his woes and fuels his desire for vengeance.
At the Charenton asylum, as Madeleine sits at the precipice of losing everything for aiding the Marquis, she begs him for one final story, which the inmates relay in a collective effort. When the last inmate, Bouchon, is moved by the tale, he breaks free and tragically kills Madeleine. The ensuing chaos sees a fire erupt in the asylum, instigated by the pyromaniac Dauphin (George Yiasoumi), allowing inmates to escape their confines.
Madeleine's lifeless body is later discovered by her blind mother in a laundry vat, while Bouchon faces his fate, imprisoned within a grotesque iron dummy. The Abbé, blaming the Marquis for the devastation, ignites a furious confrontation where the Marquis defiantly claims a deep connection with Madeleine, only to be told of her demise as a virgin. In a fit of rage, the Abbé punishes the Marquis by cutting out his tongue. In a surreal dream sequence, the Abbé descends into necrophilia with Madeleine's corpse. Though physically diminished, the Marquis remains undeterred in his artistic pursuits, even decorating his cell with a narrative penned in excrement.
In a tragic climax, during the Abbé's final rites, the Marquis swallows a crucifix while attempting to kiss it, ultimately choking and committing suicide.
A year later, the reign of the new Abbé du Maupas (Alex Avery) begins at Charenton, now transformed into a hub of literary production, employing the inmates as the staff. The works of the notorious Marquis de Sade are printed, infusing the institution with irony as his provocative narratives continue to resonate. At the end of this new journey, the new Abbé meets his predecessor, who, still confined to the Marquis's old cell, expresses a yearning to write, yearning for paper and a quill—only to find hope when Madeleine’s mother delivers them through the newly opened peephole, prompting the next chapter to unfold as he feverishly begins to write, with the spirit of the Marquis echoing within his words.
