Operation Mumbai purports to be the story of Pakistani terrorist Ajmal Kasab who was hanged earlier this week. The film traverses the journey of Ajmal, along with a fellow terrorist as they barge into one of Mumbai's main railway stations, Chhatrapati Shivaji Terminus, and open fire at the crowd, killing several people.
The story follows the route taken in reality by the two terrorists who then move to Cama Hospital where, again, they fire at the crowd killing and injure many people. Later they move out from the hospital only to run into police officers whom they shoot down.
While in the ensuing the shootout Ajmal's colleague is shot dead Ajmal himself is captured by a brave police constable. Jailed and interrogated, he refuses to talk, despite being tortured by the authorities.
Meanwhile, due to the wide publicity given to the captured terrorist, a woman in Pakistan identifies him as a Pakistani. Ajmal's handler, Akka tracks the woman down and kills her, thereby sending a warning that if anyone dared to identify Ajmal as a Pakistani, he/she would be killed.
Officer Khan (Shahbaaz Khan) is brought in to interrogate Ajmal. He uses third degree to force him to speak and Ajmal soon narrates the story of how he was inducted into the terrorist camp in Pakistan and trained for the mayhem he created in Mumbai.