Kottayam Kunjachan movie is all about Koottayam Kunjachan (Mammootty) who is a small time thug who is just out of jail. He is made to leave the Kottayam district by the local theologian and go to a place where his 'wild acts' are not heard. But he soon gets into trouble with a group of workers which makes him instantaneously famous. He gets to stay with a local devout Mikhel (Innocent) who lives with his wife Aleyamma (K.P.S.C Lalitha) has two children Mollykutty (Ranjini) and Sussy (Usha). He is tricked into doing things by Mollykutty under the false pretension that she loves him.
What happens next when he finds that she was using him is the base of the story.