Hassan (Ayad Akhtar) is a Pakistani terrorist who has been sent to New York to blow up Grand Central Station as a suicide bomber. However, the FBI arrests his terror cell before he can commit the act. Another terrorist, Khalid (Charles Daniel Sandoval), got away before the Feds arrived and tells Hassan that they must lay low until another cell can be formed, which could take months or even years. In the meantime, Hassan has been staying at the home of his childhood friend Sayeed (Firdous Bamji), who now lives in New Jersey with his wife Sarita (Farida Choudhury), their two children, and his unmarried sister Duri (Nandana Sen).
As Hassan becomes accustomed to life in the United States, he begins to question himself as to whether to not he should go forward with his mission. Hence, the war within. He gets a job as a limo driver, and shows Sayeed's son Ali (Varun Sriram) the ways of Islam, something Sayeed had been neglecting. Ultimately, Hassan decides to go ahead with his mission. He is making the bombs in the basement of Sayeed's house when he is discovered by Sayeed and Duri. After a verbal confrontation, Hassan runs out of the house with the bombs. Sayeed calls the FBI and tells them about Hassan. Despite cooperating in every way, the FBI take Sayeed in for further questioning. Duri, in the meantime, has left the house looking for Hassan. She has figured out that he intends to blow up Grand Central Station.
Hassan tracks down Khalid at a hotel and informs him that the mission will be completed today. They attach the suicide bombs to each other, and agree to commit the act at 9:00AM. Hassan then leaves, but Khalid has second thoughts and removes his bomb. Hassan gets to Grand Central Station a few minutes before 9:00, and stands in the middle of the terminal. Duri arrives at this time and begins looking for Hassan. When the clock strikes 9:00, Hassan says "God is great", then sets off the bomb.
Many people are killed or seriously wounded in the explosion. Sarita is watching the news when she learns that Sayeed has been arrested by the FBI for harboring a terrorist, and that Duri was killed in the blast. Ali, who was also watching the news, runs to his room and begins praying. Sarita comforts him while he prays as the movie ends.