Daivathinte Swantham Cleetus revolves around Cleetus (Mammootty), a dreaded long-haired rogue. He surprises the parish priest (Siddique) by his uncanny resemblance to Jesus Christ in looks and mannerisms. He is roped in by the priest for the role of Jesus Christ for a light and sound show for their upcoming festival. His real self comes to the fore during rehearsals. The fact that he is a goon is revealed, yet the priest decides to persist with him in the belief that the experience of performing the noble character will lead to his transformation. Things change in the life of Cleetus after that. Events that occurred in the life of Jesus Christ start occurring in the life of Cleetus too. What happens to Cleetus and the people surrounding him form the rest of the story.

A young police officer investigating a series of seemingly unrelated murders thinks that there is more than what meets the eye.