Kaliyoonjal movie portrays a brother to a disturbed sister. The sister, played by Shalini, is mentally disturbed if any thing goes against her will. She is possessive of her brother and creates a havoc when she gets angry. Enter Shobhana who marries Mammootty and Dileep, who plays Shobhana's brother and marries Shalini, and problems start up in the family.

Raja, a thief, and Amar, a goonda, plot to settle in London with the money earned from a robbery. But when Raja gets arrested for killing gangster Sudarshan, Amar's ex-boss, he feels Amar framed him.

The film is about a special friendship between a boy and girl, Aby (Kunchacko Boban) and Sona (Shalini). Aby and Sona are childhood friends but they have no romance between them. It was too late when they realized their romance.