Ayyappanum Koshiyum revolves around the clash between Ayyappan (Biju Menon), a senior police officer who serves at the Attappadi police station and Havildar Koshi (Prithviraj Sukumaran), who comes to the village with a motive. Ayyapan Nair is an upright police officer and Koshiy Kurian is politically well-connected. The twist in the tale occurs when their egos clash, neither willing to give up.