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.

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.