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. A flashback of 6 months ago takes us 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. He agrees on the reassurance that he will be reinstated in the Indian army to the same post from which he was removed, which means regaining the respect of his estranged father. His only team member, Nawaz Mistry (Katrina Kaif) helps him find his first target-Sajid Mir (Mir Sarwar) at the British England Cricket Match, and thus on determines his identity after breaking into his house and rigging up an explosion which makes the headlines.