The first part of the film is set in 1792, as Spain reels amidst the turmoil and upheaval of the French Revolution. Francisco Goya is a renowned painter, who, among others, does portraits for the royal family as the Official Court Painter to the King and Queen.

The Spanish Inquisition is disturbed by part of Goya's work. Brother Lorenzo is hiring Goya to paint a portrait and defends him, saying that his works are not evil, they just show evil. He recommends the Church step up the fight against anti-Roman Catholic practices. He requests and is put in charge of intensifying the Inquisition.

When posing in Goya's studio, Lorenzo asks Goya about a the young model he uses, Ines (Natalie Portman), daughter of a rich merchant, Tomas Bilbatua (Jose Luis Gomez). Ines is spotted by Inquisition spies (trained by Lorenzo) declining a dish of pork in a tavern. The Holy Office of the Inquisition orders Ines to come to the Office. There she is arrested and accused of being a heretic and practicing Jewish rituals, because she did not eat pork the other evening. She is tortured ("put to The Question"), confesses, and is imprisoned.

Tomas begs Goya for help, who in turn asks Lorenzo to find out about Ines' situation. He visits her, telling her that he is about to help her, then rapes her. At a dinner in Tomas' home, where he and Goya are guests, Lorenzo reports to Tomas that he visited Ines and that she loves her family. Lorenzo defends "The Question": he argues that if the accused is really innocent, God will give him or her the strength to deny guilt, so a person who confesses must be guilty. Tomas does not agree: he argues that people will confess to anything under physical torture, and Goya agrees. To prove this Tomas draws up a statement which says that Lorenzo confesses to be a monkey, and, with the help of his sons, does not let Lorenzo leave unless he agrees to sign it. Goya pleads for Lorenzo without success; Goya is allowed to leave and does. They torture Lorenzo and he signs. Tomas promises to destroy the document after Ines is released. He gives Lorenzo a large amount of gold for the Church, hoping it will persuade the Holy Office to consider leniency.

Lorenzo pleads for Ines, but the Church, while accepting the money, refuses, since Ines has confessed. Tomas sends the document to the king Carlos IV. Lorenzo is now an embarrassment to the Spanish Church and is banished. He flees. Lorenzo's portrait is confiscated by the Church, and is set on fire in public.

Fifteen years pass, and Goya is at the height of his creativity, but he has become deaf. The French army under Napoleon invade Spain, and abolish the Inquisition and set the prisoners free, and Lorenzo becomes Napoleon's chief prosecutor against his former Spanish allies. Ines, who was said to be tried, has actually been left to perish in the dungeons until now. She has given birth to a daughter in prison, and turns to Goya for help in finding her child, who was taken away from her immediately after birth. Lorenzo is the father, which is embarrassing for him, and he sends Ines, whose mental sanity has suffered in prison, to an asylum. Lorenzo looks for their daughter, and finds her name is Alicia, who has run away from a monastery a few years ago. In a park, Goya finds a prostitute named Alicia (also played by Natalie Portman) who looks identical to Ines. He goes to Lorenzo asking for Ines so he can reunite her with her daughter. Lorenzo goes to see Alicia, asking her to leave Spain for America, but she refuses. Goya finds where Ines is, and bribes the manager of the asylum to release her. Lorenzo arrests a group of prostitutes in an inn, including Alicia, to deport them to America. Ines finds an abandoned baby of a prostitute in that inn afterwards, and holds the baby as her own daughter.

The English conquer the French troops. Lorenzo is arrested as he is fleeing. The English reinstate the Inquisition, which sentences Lorenzo to death. The Church officials are willing to save him if he repents, and they urge Lorenzo to do so until the last moment at the site of the execution in the city center. Meanwhile, Ines is present in the crowd with the baby and calls Lorenzo enthusiastically to show him their daughter. Alicia watches the spectacle from the balcony of City Hall with her new fiance, a British officer who rescued her from the slave caravan before it reached the ships bound for America. Lorenzo refuses to repent and is executed. The film ends with a cart taking Lorenzo's body away, escorted by Ines and the baby, with Goya following behind calling to her.

• Official Movie Web Site

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