Thilakkam movie is about Padmanabhan Master (Nedumudi Venu) and his wife Devaki (K.P.A.C Lalitha) wait for Unni, their only son who is missing for many years. 10 year old Unni got lost in the crowd during a temple festival where he was along with his neighbour Panikkar (Oduvil Unnikrishnan). Panikkar too did not return since he decided to return only after finding Unni. Ammu (Kavya Madhavan) is Panikkar's daughter who also believes, like master and his wife, that her father will return one day with Unni.
Panikkar finds Unni and brings him back to the Village. The villagers realizes that Unni is abnormal and is mentally challenged. He behaves like a small boy and creates all sorts of trouble for the villagers and his parents. He is given Ayurveda treatment under the guidance of the church priest (Jagathy Sreekumar). Ammu looks after Unni, which her cousin (Nishant Sagar) objects to, as he loves her.
But finally Unni gets back his memory only to let out the truth that he is not Unni but Vishnu, the son of a Bangalore don.