Nattukku Oru Nallavan is the story of an honest police officer (Rajinikanth) and his fight against a dreaded criminal named Dddy (Anant Nag) who indulges in organ transplant mafia.

The story begins with Kunjidhapadam (Aravindan) who comes from a small place to the city for an interview and he manages to find place to stay with his distant relative Subramanyam who is actually a defaulter on loans taken on interest. He is absconding but then leaves his key at a secret place. Kunjidhapadam takes the key and stays and he also manages to get a job. On the other hand, there is Angel (Charmy Kaur) who grows as an orphan and works with a mineral water company. She doesn’t have a place to stay so she locates those houses without occupants and stays there for a night and gets going in the morning. One such instance gets her to Kunjidhapadam’s house. All this apart, there are two dons Pavadai (Kota Srinivasa Rao) and Vembuli (Jayaprakash) who are out to kill each other and Vembuli is successful in killing Pavadai’s son. So he vows to kill Vembuli’s son by the 12th day ceremony of his son. A twist of fate occurs and Pavadai’s goons mistake Kunjidhapadam to be Subrahmanyam and get him to take money. Kunjidhapadam gives an idea to kill Vembuli’s son and he is given a 16-day deadline to kill else Pavadai threatens to kill him

The CBI is in search of Sooriyan, an intelligent security officer of central ministry, who is accused of murdering a central Minister. But he has taken shelter in a remote village.