Prajapathi movie is all about Devar madom Narayanan (Mammootty) is accused to kill is father, for being cruel to his mother, at the age of 13 and serves sentence in a juvenile home. When he returns, he becomes leader of the people of Perumalpuram village. His enemies are his uncle Kunjambu Nair (Nedumudi Venu) and wife Indrani (Seema). Kunjambu Nair hated Narayanan for killing his brother. Although Kunjambu Nair and his son Giri (Siddique) tried in many ways to kill Narayanan.
At one point Giri almost succeeded in killing Devar madom Narayanan. But Narayanan again didn’t react. He was in good terms with Kunjambu Nair’s daughter (Sandhya (actress)|Sandhya) and his Murapennu (Aditi Rao).
Finally it turns out that Kunjambu Nair was the one who actually killed his father for their wealth. Narayanan helps Ali Raghavan (Sreenivasan), the real son of Kunjambu Nair, to gain his birth right. When Giri finds that he is the stepson of Kunjambu Nair, he kills his stepfather. But the family drives him away from home with the help of Narayanan. Rest of the film is about how and if Giri take revenge on Narayanan.