In the tumultuous year of 1792, Spain is gripped by the turbulence of the French Revolution. Francisco Goya, a celebrated painter, is tasked with capturing the likenesses of Spain's elite as the Official Court Painter. Yet, his artistry becomes a point of contention for the Spanish Inquisition, which takes issue with some of Goya's provocative works.
When Brother Lorenzo Casamares, portrayed by Stellan Skarsgård, comes to Goya's defense, he later enlists him to paint his portrait. Lorenzo argues that Goya's art is not malicious but merely reflects the darker aspects of humanity. He urges the Church to combat anti-Catholic sentiments more aggressively and is granted authority to intensify the Inquisition's activities.
During the portrait sitting, Lorenzo observes a painting of Inés, the daughter of wealthy merchant Tomás Bilbatúa. Shortly thereafter, Inés is apprehended by Holy Office spies—trained by Lorenzo—for allegedly "Judaizing" by refusing to eat pork. She endures a harrowing ordeal involving torture until she confesses and is subsequently imprisoned.
Her desperate father turns to Goya for assistance. In a complex game of deception and desire, Lorenzo visits Inés in her dungeon cell, offering her a semblance of comfort, yet he is internally conflicted by his lust for her. She prays with him, embodying a moment of fragile hope.
Later at a dinner hosted by the Bilbatúa family, Lorenzo passionately defends the use of torture, claiming that innocence will be upheld by divine intervention. In contrast, Goya and Bilbatúa assert that coerced confessions do not imply guilt. In an act of retaliation, Bilbatúa subjects Lorenzo to the same torture he endorses, forcing him to confess to ridiculous claims, including that he is a monkey. As a pact for Inés's freedom, a hefty donation is offered to the Church, but it is all in vain as the Inquisitor-General, Father Gregorio, refuses to release her.
In an abhorrent twist, Lorenzo again visits Inés under the pretense of prayer, but he commits the atrocity of raping her. Meanwhile, the document of Lorenzo's ludicrous confession finds its way into the hands of King Charles IV, who finds it amusing yet solemnly promises to consider Inés's plight. However, when the Holy Office comes to apprehend Lorenzo, he narrowly escapes, and Goya's portrait of him meets a grim fate as it is burned publicly.
Fast forward fifteen years, Goya—now deaf—finds himself at the pinnacle of his artistic expression. The invasion of Spain by French forces results in the eradication of the Inquisition and the liberation of its prisoners. Lorenzo, having fled to France, has become a fervent supporter of the French Revolution, now prosecuting his former comrades in the Inquisition. This ideological shift echoes the historical character Juan Antonio Llorente, who also turned against the Inquisition.
Inés, however, languishes in a dungeon—the ravages of time have taken their toll on her sanity. After giving birth to a daughter whose fate remains unknown, she returns to find her family dead and implores Goya for aid in locating her child. Unbeknownst to her, Lorenzo is the father, and he subsequently commits her to an asylum to conceal his shame.
While on a quest for his lost daughter, Lorenzo learns from the Inquisitor-General that any child born in captivity would have likely been abandoned. As Goya sketches in a park, he encounters a prostitute named Alicia, who bears a striking resemblance to Inés. Driven by compassion, he seeks to reunite Inés with her daughter, but Lorenzo, ever fearful, attempts to persuade Alicia to leave Spain instead.
Tragedy unfolds when soldiers—under Lorenzo’s orders—raid a tavern where Goya attempts to spirit Inés away, capturing the prostitutes and putting their fates in jeopardy. Amidst the chaos, the mentally deteriorating Inés stumbles upon a newborn left behind during the raid, mistaking it for her lost child.
As the tides of war turn against the French, the British, bolstered by Spanish allies, press on. The desperate state of affairs leads to Lorenzo being caught as he attempts to escape. As Spain reinstates the Inquisition, Lorenzo faces a trial that flips their roles, with the former Inquisitor-General now urging him to repent as he is led to execution, draped in a sanbenito adorned with flames—a symbol of his eternal damnation.
On the gallows, Lorenzo notices Alicia, now beside a British officer, openly mocking him. Inés emerges from the crowd, revealing the child she believes to be their daughter—a poignant moment filled with twisted irony. Despite pleas for repentance, Lorenzo remains defiant as he meets his grim fate, the dose of justice served cold. The film concludes with a haunting image of Inés carrying his child while Goya, heartbroken yet resolute, trails behind, calling for her, and she glances back, a fleeting smile gracing her face, before walking alongside the cart bearing Lorenzo's lifeless body.
