Kottayam Kunjachan is about an erstwhile thug, who has just been released from jail. He has served a sentence of 7 years, for killing a man in a fight gone bad.After an altercation with his previous employers, he is arrested and later bailed out by his guardian, a Christian priest who found him as an infant in a garbage heap and raised him as his own. Following his father's advice, he leaves Kottayam and its bad influences for Odaangara. He starts a technical institute, accompanied by Bosco, his assistant. He generally endears himself to the village populace. It is there that he meets Mikhael and his wife, and gets in their good books by rescuing Mollykutty from a kidnap attempt by Jimmy and gang. leyamma convinces Mikhael to rent out their outhouse to Kunjachan, as a deterrent from further attacks by Paappan or Jimmy. Mikhael then convinces Kunjachan to go to confession, and start living as a good Christian.
