Set in a small village, the story of Varikkuzhiyile Kolapathakam revolves around the life of a young Parish priest, Vincent Kombana (played by Amith Chakkalakkal) and the 40 families that live in the village. The father is smart, loving, and affectionate towards the people and in return, they too respect and love him a lot. All goes well for the villagers, until, one day the father witnesses a murder in the village post which the criminals keep the father locked up in a secret location to hide the crime. Will the priest reveal the truth to the villages? Will he bring the criminal to justice?