Rizwan Khan, a Muslim from the Borivali section of Mumbai, has Asperger's syndrome. He marries a Hindu single mother, Mandira, in San Francisco. After 9/11, Rizwan is detained by authorities at LAX who treat him as a terrorist because of his condition and his race.

Arun is an Indian undercover agent enlisted to stop ISI chief Ishaq Khan. The village girl Reshma helps him but endangers her own life.