The movie begins with a car chase in Chicago, which leads to a scuffle between a man ostensibly named Jude Rosario (Saif Ali Khan) and an American male known as Matthew Broody. The scuffle ends with Broody falling into the icy waters of Chicago River, and his body missing. This results in Rosario being arrested and convicted of murder.

A flashback of six months ago shows the office of the Indian RAW chief Roy (Sabyasachi Chakrabarty), where he and his trusted men (Rajesh Tailang, Mohammed Zeeshan Ayyub) plan a daring covert operation. The man, known as Jude Rosario in the opening sequence, is shown to be Captain Daniyal Khan, a dead-end ex-soldier with a completely deadened sense of life and death who is pulled out of oblivion and pressed into service by the spy agency to wreak vengeance on the men who planned the 26/11 Mumbai terror attacks. He agrees with the assurance that he will be reinstated in the Indian army to the same rank from which he was court-martialled, which meant regaining the respect of his estranged father and mentor, Dilawar Singh. His only team member, Nawaz Mistry (Katrina Kaif) helps him find his first target Sajid Mir (Mir Sarwar) at a cricket match in London. On reaffirming his identity after breaking into his apartment, Daniyal rigs up an explosion which kills Sajid, which makes the headlines explaining it was accidental, causing an investigation by the Pakistani ISI.

Coming back to the present, Daniyal aka Jude has landed in the same jail as David Headley (J. Brandon Hill), his next target. He contacts Nawaz, in order to acquire money to buy a battery, as a replacement of another one which holds a certain poison. The poison is untraceable as it could kill a person whose tongue even comes in contact with it with a heart attack. After killing David Headley by plugging the poisonous battery into a showerhead he usually uses, Matthew Broody, who supposedly died upon falling in the river, is found alive and Daniyal is released as his earlier sentence is rendered null and void. Meanwhile, ISI agents gather information about him.

Daniyal and Nawaz, through Syria, go to Pakistan to take down the last two perpetrators, Sahabuddin Umvi and Haaris Saeed (Shahnawaaz Pradhan). There, they make plans of killing Saeed with the help of local restaurant owner and sleeper agent Khalid (Middat Khan), by an explosive planted in the mic used during his public rally. However, their plan fails to lead Daniyal to pursue Saeed in a car and shoot him dead, also causing an explosion. Umvi is killed with the help of a nurse Amina Bi (Sohaila Kapur), a mother who lost her militant son in a suicide attack, who replaces his regular syringe with one with poison.

With the Pakistani army and ISI pursuing them, Daniyal and Nawaz make their way to the coast to escape through the Arabian Sea. Their accomplices get caught and interrogated for information or killed. While they are escaping on a boat, the Pakistani military finds out about it and sends patrol boats to apprehend them. While hiding in the waters with Nawaz, Daniyal gets shot by the military and dies, while Nawaz later gets rescued by the Indian Navy, after they leave. Later, she goes to the Taj Hotel and has two cups of tea, fulfilling a promise earlier made to Daniyal.