Kanyakumari Express movie tells about an Assistant police commisioner Mohan Sanker (Suresh Gopi). He lost his wife and children in an accident and shifted his job to Crime Branch. He did this only to lead a calm life. Change in in his duty was welcomed by some politicians. But he was carrying his duty secretly that too without uniform.

He even did research on temples of Kerala and Nanchinad. It was during this period his enemies began to die one by one. The Chief Minster (Jagathy Sreekumar) too misunderstood Mohan Sanker for the death of his enemies. There he started to investigate those murders.