Rasathanthram tells the story of Premachandaran(Mohanlal) who is a carpenter with a few secrets and lives along with his father Balan Master(Bharath Gopi) and works along with his friend Manikandan (Innocent). They are now working in a house near the house of a rich landlord. Kanmani (Meera Jasmine), who was sold by her mother works in that house as a servant and is ill-treated.
One night, Premachandran goes to his workplace to take his tools. He sees Kanmani moving out of the house and gets puzzled. He follows her. She was on the verge on committing suicide. he decides to save her from the hell and promises her a job somewhere far away.
But the police are looking for her everywhere and he had to hide her somehow. That is when they chance upon the idea of disguising her as a man. Kanmani fall in love with Premachandran but he doesn’t reciprocate—she couldn’t understand why; that is when Premchandran reveals his bitter past.