Thuppakki story begins with Jagdish (vijay), a captain with the Indian army and he is keen to flush out the ‘sleeper cells’ in the country. He gets engaged to Nisha (Kajal Agarwal) who hails from his village. The story takes a turn when Jagdish goes to Mumbai and a bomb blast occurs. He starts his hunt to chase the culprits and catches one of them only to discover that there are more of such bombs in the city. How Jagdish goes about tracking the other bombs and the people behind it form the rest of the story.