Phantom begins with a car chase in Chicago, which ends with a man plunging into the icy waters of a river. Daniyal Khan (Saif Ali Khan) is convicted for murder and jailed. Cut to the office of the Indian R.A.W. chief Roy (Sabyasachi Chakrabarty), where he and his trusted men (Rajesh Tailang, Mohammed Zeeshan Ayyub) plan a daring covert operation. Daniyal, now a dead-end ex-soldier with a completely deadened sense of life and death 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.
The R.A.W. chief who orders the killings does not have the permission of the home minister and hence he has to keep everything under wraps. The reclusive Daniyal fits his plan like a glove. Daniyal then went on to kill the 26/11 attacks perpetrators- Sajid Mir, David Coleman Headley, Sabahuddin Umvi and Hariz Saeed.