Pithamagan whirls around four characters. Chithan (Vikram) who is orphaned at a young age, devoid of all human contacts he lives on his animal instincts and ekes out a living as a graveyard caretaker. He seems to exhibit behaviour consistent with autism spectrum disorders. Gomathy (Sangeetha), a petty ganja seller, who pities Chithan’s condition, gets him a job at the ganja fields of the main villain. Sakthi (Suriya Sivakumar), the conman cons Manju (Laila), a polytechnic student but does not get away with it. Sakthi meets Chithan in jail and takes pity on him and befriends him. It is Sakthi’s affection that melts Chithan’s stony heart.

Sakthi takes Chithan along with him when they are both released from the jail. Sakthi and Manju later fall in love. Chithan works for a narcotics dealer, who is the antagonist. The dealer takes advantage of Chithan's innocence and orders Chithan to burn the corpse of a spy. Sakthi is angered when he discovers that Chithan had burned the corpse, as this could land Chithan in trouble. Sakthi requests Chithan not to work for the narcotics dealer anymore and takes Chithan along with him to work. This angers the villain and he eventually kills Sakthi when he return home with Manju after watching a movie. The next morning Sakthi's corpse is thrown in the middle of the village. Initially it seems as though Chithan is unaffected due to Sakthi's demise while the rest are mourning. Gomathy chases Chithan out of her house as she feels that it's because of Chithan that Sakthi was killed and it has not even impacted him. Chithan leaves the house and sets the ganja fields on fire and then goes to the villain's house and beats him black and blue. He then drags him to the village and kills him in front of Gomathy, Manju and the other villagers. He looks at Manju after killing the villain which moves Gomathy and she feels guilty as she mistook Chithan's silence when Sakthi was killed. She tries to persuade Chithan to stay with them but Chithan goes back to the graveyard where Sakthi was buried.

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