An Afghani Al-Qaeda Jihadi Omar (Rahul Bose), his accomplice Salim (Jaideep Ahlawat) and their international terror network, plots to attack New York with a "Cesium-bomb". Vishwanath alias Wiz (Kamal Haasan) is a Kathak teacher who lives with his wife Nirupama (Pooja Kumar), a nuclear oncologist, in New York. Nirupama confides with a psychologist that its a marriage of convenience that provided her a safe haven for pursuing her Ph.D in the U.S.A. The age gap between them notwithstanding, she is put off by Vishwanaths effeminate traits and is attracted to her boss, Deepak (Samrat Chakrabarti). Doubting whether her husband has secrets of his own, she hires a private investigator to trail him. She learns from the private investigator that Vishwanath is not a Hindu but a Muslim. In a sudden turn of events, the investigator gets killed by Farukh, a prominent member of the terrorist outfit led by Omar. A business card on his wallet gives away Nirupama and the terror group led by Farukh nabs the couple. The outfit operates from a warehouse on the outskirts of the city where the couple is being interrogated. It is revealed that Deepak was ensuring funds for the jihadi sleeper cell.
Vishwanath is involved in a fight with the terrorists, kills Farukh and his men at the warehouse and escapes with Nirupama. Omar and Vishwanath have a past, one that takes the story back by almost a decade, to the Al-Qaeda training camps in Afghanistan. Vishwanath alias Wisam Ahmad Kashmiri was one of the trainers in the Al-Qadea terror camps across the Durand Line. It also showcases Inter-Services Intelligence support to the terror groups. Wisam is shown as a jihadi in Kashmir, wanted by the Indian Army, who fled to Waziristan. He doesn't know Pashto, but knows Hindi. It also shows American forces attacking Afghanistan. What follows is a maze of events that go back and forth in time, unraveling a plot where in the terrorists are accumulating cesium from oncology devices to trigger a blast in New York.
Nirupama is stunned to discover the true identity of her husband Vishwanath, his uncle (Shekhar Kapur), American accomplice Dawkins (Miles Anderson) and the young dancer Ashmita (Andrea Jeremiah) at her husbands dance school. Vishwanath is revealed to be Wisam Ahmad Kashmiri, an Indian Muslim RAW agent who married Nirupama to investigate Deepak and his boss Omar in connection with a bomb blast in the heart of New York. He had assassinated many prominent terrorists in Afghanistan, including Nassar (Nassar), Omar's boss. His mission is to bust the sleeper-cell of the Jihadis in the United States of America, which is planning to divert the attention through "capsules" capable of emitting mild nuclear radiation tied to pigeons in New York city while enabling Abbasi, a Nigerian suicide bomber to detonate the cesium bomb in the city.
Together, the team try to counter the plans of Omar and his group that could destroy the most of the New York city. In the ensuing events, Vishwanath is arrested by the FBI before being rescued by his uncle and Dawkins is murdered by Salim. Angered by this murder, Colonel Jagnath, Wisam's boss, goes after Omar and Salim. The Prime Minister of India directs Wisam to take any step to avert the catastrophe. Wisam along with the FBI, take down Abbasi and defuse the Ceasium bomb. Omar and Salim try to escape in a plane. Omar tries to activate bomb through his phone, but failed. He then called Abbasi, but call is attended by Wisam, who tells him that Abbasi is not alive, Omar is shocked to hear this but escapes with Salim in his plane. The film ends with Wisam indicating that he would now go after Omar alluding to Vishwaroopam 2 set in India.