Fiza narrates the story of a sisters Fiza (Karisma Kapoor) single-minded search of a missing brother. It also dwells on how the search affects the socio-political and religious favour of the land. Nishatbi (Jaya Bachchan) is a widow and mother of Fiza and Amaan (Hrithik Roshan). Fiza loves Anirudh (Bikram Saluja) while Amaan is in love with Shehnaz (Neha). A riot breaks out between the religious groups and Amaan disappears. People believe that he is dead. Fiza feels that he is alive and starts searching for him and in the process she encounters strong opposition from both the religious groups who want to exploit Fiza for political reasons. Later she discovers that Amaan is alive and joined a group of terrorist lead by Murad Khan (Manoj Bajpai). He does not want to return as he had killed some people while saving his life and he feels that he would not get justice. But on Fiza's insistence, he returns home. He does not get a job and Shehnaz gets married. He returns back and finds out that Murad Khan is also using him. He does not want to get killed either by the police or the terrorist, hence he asks Fiza to eliminate him.