Natturajavu movie is all about Pulikattil Charlie (Mohanlal) who is a tough but easy going guy who owns a quarry and an estate. His late father Pulikattil Mathan (Ramraj) has left behind a lot of problems for Charlie. Mathan had created quite a few enemies who are trying to get even with Charlie now.
Mathan was a terrible person and practically no one liked him and no one had anything good to say about him even after his death. Charlie is trying to live a low profile life but is forced to sort out the mess created by his late father. He is living with his mother( Kaviyoor Ponnamma), grandmother (KPAC Lalitha) and a younger sister Katrina (Nayanthara) who is an illegitimate child of Mathan.
Charlli had another brother Samuel (Sarath) who committed suicide a while ago due to Mathan's harassment. Samuel's wife Rosy (Suja Karthka) and her child also live with them.
Karnan ( Ranjith) who is one of the powerful enemies of Mathan. Karnan had killed Mathan and he is serving time in jail and hopes to be free some day. In order to avoid future problems from Karnan, Charlie had married Karnan's beautiful sister Maya (Meena) but Karnan is not happy about this alliance either. Karnan is determined to take revenge on Mathan's family and Charlie is a part of it. But Charlie handles these situations very boldly.