The film tells the story of Alphonso, a man who chooses to suffer a slow, torturous life in his little village, Mahe, in preference to fortunes and pleasures away from it.

Sonia, the daughter of a rich father, is in love with Sunny, an orphan. Her father knows that Sonia is in love with Sunny but doesn't quite favour him because of his poor financial status. Things go upside down when a mentally unstable girl enters the life of Sunny.

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 skit on Jesus Christ brings out a change in good-hearted rowdy Cleetus along with revealing few surprises of his nature and his relationship with a neighborhood tailor.