Plot

Zubeidaa, an aspiring Muslim actress, marries a Sikh prince to become his second wife. Her tumultuous relationship with her husband, and her inner demons lead her to a decision which has fatal consequences for them all.

The film begins with Riyaz (Rajat Kapoor), Zubeida's son setting out to research her life, and to meet the people who knew her. The story is thus told in the form of memories/reminiscences. Zubeida is a Muslim actress, who's career aspirations are thwarted by her film-producer father (Puri) who looks down upon a woman in acting. He arranges her marriage to her friend's son, but that breaks up after the birth of her son. Zubeida is now back at her parent's home, sad and depressed. Rose (Lilette Dubey) her father's mistress tries to cheer-up Zubeida by taking her out. On one of these outings, Zubeida meets Prince Vijayendra (Victor) Singh of Fatehpur (Bajpai). Quite taken with her, the Prince woos and marries her. Zubeida, now the 2nd wife of a Hindu prince, leaves her son behind with her mother (Sikri) and comes to live at Fatehpur. Here she meets the much older Mandira Devi (Rekha) the Prince's first wife, learns about the etiquette of being a Rani, and of the duties her husband has towards his first wife. Zubeida's relationship with Mandira (whom she calls Mandy didi) is tumultuous, seesawing between affection and jealousy. She frets about the restrictions on her as Rani and the choke-hold of royal duties on Victor, often venting out her frustrations at not having her husband to herself. When Victor decides to contest the elections, he relies on Mandira, as his Hindu consort (as opposed to Zubeida), to accompany him on his political jaunts. Zubeida, angry at being spurned, in obstinacy takes a decision, which has fatal consequences.—Amodini

Zubeidaa is the story of Riyaz's (Rajit Kapoor) search to understand his mother, who is not known to him, as he was brought up by his grandmother in the absence of his mother. His mother's name was Zubeidaa (Karisma Kapoor) and she was the only daughter of a filmmaker named Suleman Seth (Amrish Puri) & his wife Fayyazi (Surekha Sikri). Riyaz is taught from childhood that his mother died in a plane crash, but her name is not discussed by anyone in his house.

Riyaz now is grown up and decides to looks for prints of his mother's movie "Banjaran Ladki". Tracing the studios, he finds Dance Master Hiralal (Shakti Kapoor), who tells Riyaz the story of how Zubeidaa got interested in films, when she visited the studio with her dad. Rose Davenport (Lillete Dubey) was Suleman Seth's mistress and Zubeidaa's dance teacher. Suleman sold the studio to Nandlal Seth (Harish Patel). Suleman was against Zubeidaa acting in movies and interrupted her first day on sets, else she would have made it to the top. For the movie print, Hiralal points Riyaz to Rose.

Zubeidaa acts in films secretly, but when her father finds out he forbids her to carry on and quickly arranges her marriage to Mehboob Alam (The son of Suleman's friend Sajid Masood). Zubie is not happy as she wanted to go to finishing school to Switzerland. But Fayyazi convinces her that her dad wants good things for her. Soon, Zubie is married. Things look happy for her when she gives birth to Riyaz. However, a misunderstanding arises between Suleman Seth and Mehboob's parents, and Mehboob divorces Zubeidaa few days after she gives birth. Basically Sajid wants to go back to Pakistan as he is discouraged by the treatment meted out to Muslims in India. Suleman disagrees with this as says he has pulled all his connections to get Mehboob a permanent job at the govt hospital. Things get so bad that Suleman tells Sajid that he wont allow Zubie and her kid to leave with them to Pakistan.

Riyaz meets Rose. Fiyyaz blames Rose for Zubie's death, bot Rose says that Zubie was unhappy and all she did was to bring some happiness into her life. Zubeidaa then meets Maharaja Vijayendra Singh (Victor) of Fatehpur (Manoj Bajpai) at a polo game, mediated by Rose. Victor lusts after Zubie and meets her many times. Fiyyaz is not happy with this match, as she thinks Victor is only taking advantage of Zubie. Fiyyaz meets Victor and understands the situation and that Zubie will be the junior queen and would have rights accordingly. Victor is ready to adopt Riyaz, but Fiyyaz wants Riyaz to be brought up in a Muslim house and asks Zubie to leave her behind, as a condition for her acceptance. Then one day he takes Zubie in his royal plane to Fatehpur, leaving Riyaz behind.

Vijayendra is already married to Maharani Mandira Devi (Rekha) and is the father of two children. Nevertheless, he falls in love with Zubeidaa and they get married, but there is continuous turmoil in their relationship. Riyaz pesters Fiyyaz for Zubie's journals which she wrote while she was at Fatehpur.

Riyaz learns through Zubeidaa's journal that though she loved Vijayendra dearly, she was unable to follow the mainly Hindu customs and traditions of the palace (which Mandira teaches her, but Zubie finds them stifling for her personality) (Also she is angry at being treated as the junior queen), being a Muslim. She was also uncomfortable because of her brother-in-law Uday Singh's (Rahul Singh) sexual advances towards her, and his demands of her to have an extra-marital affair with him. Uday also objects to Victor gifting a side palace to Zubie and accuses him of bias and ignoring the populace. Away from her own family, she was unable to enjoy the beautiful surroundings of the palace.

Riyaz travels to Fatehpur palace (which is now a hotel) and asks many people about his mother. However, all except Mandira, whom Zubeidaa called "Mandy Didi"' deny that his mother ever existed, or say that she was a horrible woman who seduced their king and caused his death in a mysterious accident.

On reading the journal, Riyaz finds out that Vijayendra had become a politician (he was being instigated by other Royal kings to rebel against the Indian Government, but Victor did not want to be branded as a traitor. Uday was not in favor of Victor meek submission and wanted to fight for his rights), and was about to go to Delhi for an important meeting. Zubeidaa felt frustrated that whenever her husband needed help he looked to Mandira for support (Mandira was working with Victor full time on the election campaign. Zubie feels that Victor is ignoring her as he is bored of her), and at the last minute she insisted that only she will go for the meeting (with the Cong high command to discuss the possibility of a joint government after Victor's party has won 40 seats in state elections).

In the end, Riyaz and his grandmother watches a tape of one of his mother's films with his family. Though he loves his mother very much, Riyaz never succeeds in deciphering the mystery behind his mother's demise (Did she crash the plane herself or was it a conspiracy from Delhi). It is left to the audience to decide how she died.