Part 1
Part 2

Anniyan is the story of Ramanujam "Ambi" Iyengar (Vikram), a brahmin lawyer who suffers from Multiple Personality Disorder. Ambi is an innocent and honest lawyer. If he comes across anyone not obeying the rules he files cases against them but all his efforts go in vain.

His constant habit to be perfect in rules and honesty leads him to develop a Multiple Personality Disorder in which a new character in him grows as anniyan (Vikram) and starts a website called www.anniyan.com [www.aparichit.com in the Hindi version] to hear people's complaints. This anniyan is a violent man and the Ambi in him whenever he comes across a person who does not obey rules he makes complaints in his website. When he is Anniyan, he goes and kills them by methods used for torturing people in hell. He apparently takes the definition of these methods from the Garuda Purana.

During the first half, Anniyan kills 3 different people due to their actions:

* A man who did not stop to save a person in critical condition. Anniyan forces a herd of buffaloes to stampede him to death. He calls this murder "Anthakoopam", a Sanskrit word and one of the punishments in the Garuda Purana.
* A chef who fails to provide decent food for railway passengers. Anniyan tosses him into a pot and frys him to death. This punishment is called "Kumbhipakam". The chef was the brother of DCP Prabhakar (Prakash Raj) and the death caused Prabhakar to rise with anger, promising to kill his brother's murderer when he is found.
* A factory owner who makes faulty motor parts. He sends a group of thugs to kill Ambi, but this triggers Anniyan, who knocks out all the men. Later, Anniyan ties the owner to a tree and dumps leeches onto his body. This punishment is called "Krimiibhojanam"

Meanwhile, DCP Prabhakar and Chari (Vivek), a friend of Ambi, are after the murderers.

Ambi is in love with his neighbor Nandhini (Sadha). After she rejects him, Ambi develops another personality, a ramp walk model named Remo. Nandhini instantly falls for Remo and his tricks.

Later, Nandhini acquires land, but tries to cheat the government out of taxes. Ambi chooses not to help her, but when Nadhini tells Remo, Anniyan takes over and goes after her. Just as Anniyan is about to toss her into a pit of fire, Anniyan reverts back to Ambi. He is admitted to a hospital where he is diagnosed with a multiple personality disorder. It is at this hospital that Ambi reveals a dark secret from his past when he is hypnotized. When he was a young boy, corruption and incompetence in the police force and elsewhere had resulted in the death of his sister. After listening to this story, the doctor (Nassar) concludes that the death of Ambi's sister resulted in the development of the psychological disorder. According to the doctor, Remo will cease to exist only if Nandhini accepts Ambi's love. However, Anniyan will cease to exist only when the country is reformed. Nandhini eventually accepts Ambi's love and Remo disappears.

Ambi is finally caught and is sentenced to two years of psychological treatment at which time if he is cured, he will be released. When he is released, he relapses when traveling in a train, after a man refuses to stop drinking in the presence of ladies. Apparently, the man is the same person who indirectly, became a cause for Ambi's sister's death due to his negligence of duty. He kills the man, hiding the crime from Nandhini as the credits start rolling.