PHANTOM starts off with the visuals of the 26/11 Mumbai attack. This is immediately followed by a high octane car chase sequence between Daniyal Khan (Saif Ali Khan) and an unknown man in Chicago (US) who bangs his car and tries to drive away. Daniyal finally gets hold of him but accidentally kicks him off the bridge into the river below. This, then, leads to an array of flashback events, which establishes the connection between Daniyal Khan’s past to his present day life.
The flashback states that, after being dismissed from the Indian army, Daniyal goes into a hibernation of sorts, living an isolated and secluded life of his own. In the meanwhile, when India’s RAW (Research and Analysis Wing) learns about Pakistan based terrorist group Lashkar’s yet another plan of attacking India, they plan a secret operation, off the books, to take down all the accused and masterminds behind Mumbai attacks.
After much research they decided on hiring Daniyal Khan for this job. The RAW officials believe that Khan is like ‘Phantom’, he has no records and is completely off the radar. As a part of the mission, he meets up with the beautiful and talented Nawaz (Katrina Kaif) in UK where she works as a ‘Security Consultant’. The duo however gel well after Daniyal’s first two missions in UK and US.
Thereafter this duo’s journey traverses from Beirut, Syria and finally Pakistan. Even though Daniyal Khan’s mission happens to be a ‘top secret’ and ‘highly confidential’ one, the Pakistani officials sniff out his plan before Daniyal Khan reaches his ultimate goal of killing Hariz Saeed (Shahnawaz Pradhan), the mastermind behind the 26/11 attacks. Does Daniyal Khan become successful in his life threatening mission, why does Nawaz help him in his mission, are Pakistani authorities able to catch hold of Daniyal Khan, is what the rest of the story is all about.