Bio-scientist Govindarajan Ramaswamy speaks at the Jawaharlal Nehru Stadium about chaos theory and the butterfly effect. He begins by reciting events from the 15th century in Chidambaram, when King Kulothunga Chola II, a Saivite, persecutes Vaishnavites and intends to destroy an idol of Govindaraja. Rangarajan Nambi, a Vaishnavite, protects it and offends the king, who orders Rangarajan to be executed by being submerged into the sea with the idol, succeeding.
On 20 December 2004, a bio-technology lab in the United States designs a virus intended as a bio-weapon. After understanding its potential, Govind, one of the scientists involved, refuses to give the vial (containing the virus) away due to fear of misuse. However, his boss Sethu has other plans and tries to sell it to a terrorist group when Govind flees with it. Former CIA agent Christian Fletcher follows him and attempts to seize the vial, when it is accidentally couriered to India. Govind sneaks into the aircraft carrying the virus and changes its location. After arriving in India, he is questioned by Balram Naidu, a RAW operative. Govind unsuccessfully tries to explain the series of incidents.
Meanwhile, Fletcher, who has married a woman named Jasmine, arrives in India. Using her as a translator, Fletcher threatens Govind and takes him away in a jeep with a police officer. After exiting the city, Govind escapes from Fletcher and reaches Chidambaram. Fletcher follows him, after getting a cab, along with Jasmine. After Govind attempts to persuade the receivers of the package carrying the virus, it finds itself inside an idol of Govindaraja. In the chaos, Jasmine is killed . Govind and Andal, who is the granddaughter of Krishnaveni (Haasan), an old woman for whom the package was sent, try to run away from Fletcher, and arrive in a ground where illegal sand miners are working. They try to rape Andal, but Govind defeats them and they sneak out after the interference of Vincent Boovaragan, a social activist, and saves an unnaturally tall Muslim named Khalifula and his family from a car-crash in the process. One of them, a lady, faints suddenly and is taken to a hospital, where Govind procures a cooling box to store the weapon, as it is unstable and its temperature needs to be maintained. He meets pop singer Avatar Singh, who is also there for treatment of his throat cancer. His prescription drugs are in a similar-looking box and before leaving the hospital, he unknowingly switches it with Govind's box.
Fletcher follows them and takes Andal and the Muslim family hostage in their house, from where Govind is blackmailed to bring back the box he is carrying. With no choice, he reaches the place, only to discover that Avatar must have the weapon. The police surround the house, forcing Fletcher, Govind and Andal to flee in a jeep. Shinghen Narahazi, a Japanese martial arts expert, whose sister was earlier killed by Fletcher, follows them. Avatar finishes his last performance and discovers the blunder, only to get shot by Fletcher after having a row.
Govind and Andal flee to reach a construction site, where Govind takes out the weapon before giving the idol to Fletcher. The sun dawns on 26 December 2004. Govind gets an idea from some drainage workers to immerse the virus in a large quantity of salt to destroy it. He goes to the sea, only to be stopped by Fletcher. Shinghen Narahazi arrives and fights with Fletcher. Both Narahazi and a motivated Govind fight Fletcher together and defeat him. Fletcher opens and swallows the virus. Suddenly, a tsunami strikes, washing away Fletcher, and causing great destruction along the coast. Poovaragan's house is struck and he dies in a car after saving a child. Andal, Govind and Narahazi get into a boat. Krishnaveni arrives and begins to cry after perceiving Poovaragan as her long-lost son. After relief measures are taken, Andal argues that god had sent forth the tsunami to get rid of the weapon. Govind responds by asking if god would destroy hundreds of lives to save millions. They are later revealed to have been talking in front of the idol submerged in the 15th century. The scene shifts to the stadium, where Avatar, who had his cancerous growth taken away by Fletcher's shot, along with several others, listening to the speech by Govind, followed by former president George W. Bush as the credits roll.

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