Although the historical setting of the film is authentic, the story about Goya trying to defend a model is fictional, as are the characters Brother Lorenzo and the Bilbatúa family.
In 1792, Spain reels amid the turmoil and upheaval of the French Revolution. Francisco Goya (Stellan Skarsgård) 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 Casamares (Javier Bardem), who has hired Goya to paint his portrait, defends him, saying that his works are not evil, they just show evil. He recommends the Church step up the fight against anti-Catholic practices, and is put in charge of intensifying the Inquisition.
When posing in Goya's studio, Lorenzo asks Goya about a young model he uses, Inés (Natalie Portman), daughter of a rich merchant, Tomás Bilbatúa (José Luis Gómez). One evening Inés is spotted by Inquisition spies (trained by Lorenzo) declining a dish of pork in a tavern. The Holy Office of the Inquisition summons Inés and arrests her on a charge of "judaizing" (spreading Jewish rituals), for refusing to eat pork. She is stripped naked and tortured by strappado ("put to The Question"), confesses, and is imprisoned. The Inquisition's archives had already revealed that one of her father's ancestors had converted from Judaism to Christianity in 1624 upon arrival in Spain from Amsterdam.
Bilbatúa begs Goya for help, who in turn asks Lorenzo to find out about Inés's situation. Lorenzo visits Inés in prison telling her that he is going to help her and will pass a message to her family if she wishes. He offers to pray with Inés, but is clearly struggling with his desire to rape her as, still naked, she prays with him at his request. Later at a dinner in Bilbatúa's home, where he and Goya are guests, 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 therefore be guilty. Bilbatúa does not agree: he argues that people will confess to anything under torture, and Goya agrees. To prove this Bilbatúa draws up a statement which says that Lorenzo confesses to being a monkey, and, with the help of his sons, prevents Lorenzo from leaving unless he agrees to sign it. Goya pleads for Lorenzo without success, and is escorted away and pushed out of the home. Bilbatúa, his sons and servants torture Lorenzo with a makeshift strappado, causing him to break down and sign. Bilbatúa promises to destroy the document after Inés 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 Inés, but the Inquisitor General Father Gregorio, while accepting the money, refuses, since Inés has confessed. Lorenzo again visits Inés in prison and, offering to pray with her, instead rapes her. Bilbatúa brings the document to the king, Charles IV (Randy Quaid) who is highly amused at seeing it, and promises to assist Inés. Lorenzo is now an embarrassment to the Spanish Church and flees when they come to arrest him. His portrait is confiscated and is set on fire in public, to burn him in effigy.
Fifteen years pass, and Goya is at the height of his creativity, but has grown deaf. The French army under Napoleon invades Spain, abolishes the Inquisition and sets its prisoners free. Lorenzo had fled to France, where he was introduced to the ideas of the French Revolution and became a fanatical adherent of them. He is now Napoleon's chief special prosecutor against his former Spanish colleagues in the Inquisition. (This twist in Lorenzo's allegiance might have been inspired by the career of Juan Antonio Llorente.) A French court presides over the show trial, conviction and sentencing to death of the Inquisitor General.
Inés has been left to languish in the dungeons until now; she had given birth to a daughter in prison, who was taken away from her immediately after birth. Upon visiting her old home and finding her family killed, Inés turns to Goya for help in finding her child. Lorenzo is the father, which is embarrassing for him, and he sends Inés, whose sanity has suffered in prison, to an insane asylum. Lorenzo questions the condemned Inquisitor General, who tells him that a child born in the prison would have been placed in an orphanage. Lorenzo locates it, and he learns from the nuns who run it that his daughter, named Alicia, had run away several years before.
In Garden Park, Goya finds a prostitute named Alicia (also played by Natalie Portman) who looks identical to Inés. He goes to Lorenzo asking for Inés in order to reunite her with her daughter. Lorenzo takes the initiative and secretly goes to see Alicia, offering to pay for her passage to America if she will leave Spain. She refuses, declaring him insane. In the meantime, Goya travels to the asylum where Inés has been kept. He pays the director a bribe to release her, and then tries to bring Inés to see Alicia in a tavern where prostitutes gather. Unfortunately, as Goya tries to persuade Alicia to see her mother, a group of soldiers, under orders from Lorenzo, burst into the tavern and forcibly arrest all the prostitutes. Goya discovers Lorenzo's intention to sell the women off to America where they will be treated as slaves. Inés, waiting outside to meet Alicia, wanders into the tavern and finds a baby left there when its mother was seized in the raid. In her delusion Inés thinks the baby is her own lost daughter; she is delighted and wanders off with the child.
The British invade Spain from Portugal, defeating the French troops with the help of the Spanish population. The wagons in which the prostitutes are being transported are abandoned by the French cavalry guarding them when the British attack, with Alicia catching the eye of a British officer. Lorenzo is arrested as he is fleeing. The Spanish reinstate the Inquisition, which now tries and sentences Lorenzo to death, the Inquisitor General condemning him in much the same words as Lorenzo used at his trial. They urge Lorenzo to repent, even at the site of his execution, to which he is led in the auto da fe wearing a sanbenito with painted flames indicating he is sentenced to die. On the scaffold, Lorenzo spots his daughter Alicia, on the arm of the British officer, scoffing at him. He also notices Goya sitting at a distance sketching the entire ordeal. Inés is also present in the crowd and calls to Lorenzo enthusiastically to show him the baby she believes is their daughter. Refusing to repent, despite pleas from his former colleagues the monks, Lorenzo is garrotted. The film ends with a cart taking Lorenzo's body away, escorted by Inés still carrying the child, with Goya following closely behind her calling for her. She glances back with a smile, but continues to accompany the body as she kisses its hand.Natalie Portman as Inés Bilbatúa and Alicia
Javier Bardem as Lorenzo Casamares
Stellan Skarsgård as Francisco Goya
Randy Quaid as King Charles IV of Spain
José Luis Gómez as Tomás Bilbatúa
Unax Ugalde as Ángel Bilbatúa
Michael Lonsdale as Father Gregorio
Julian Wadham as Joseph Bonaparte
The film has grossed $2,198,929 in Spain and $1,199,024 in Italy. In the United States, Goya's Ghosts has grossed $1,000,626, with a worldwide total $9,448,082.
Goya's Ghosts received poor reviews from critics. The review aggregator Rotten Tomatoes reported that 30% of critics gave the film positive reviews, based on 87 reviews — with the consensus that "ornate costumes and a talented cast can't make up for Ghosts' glacial pace and confused plot." Metacritic reported the film had an average score of 52 out of 100, based on 25 reviews — indicating average reviews.