‘Wazir’ is a thriller flick about an anti-Terrorism Squad (ATS) officer Daanish Ali (Farhan Akhtar), who lives a blissful life with his wife Ruhana (Aditi Rao Hydari) and little daughter Noorie. One day, while Daanish is driving with Noorie, he spots a known terrorist, Farooq Rameez, driving by and chases him. Rameez and his gang ambush Daanish's vehicle and Noorie is killed in the ensuing firefight while Rameez escapes.

Ruhana is shattered and blames Daanish for Noorie's death, completely shutting him out from her life. Daanish moves to his friend and colleague Sartaj's house where Sartaj gives him sleeping pills; however, Daanish overhears Sartaj discussing Rameez's location with their superintendent SP (John Abraham). Unexpectedly, Daanish then turns up at Rameez's location while a police operation is ongoing and starts a shootout, eventually killing Rameez. The ATS bosses are enraged as they wanted to capture Rameez alive and find out which politician intelligence sources say he was in Delhi to meet. Daanish is sent away on medical leave.

A grief-stricken Daanish is about to kill himself at his daughter's grave when a mysterious van appears, driving off when Daanish yells at it. Daanish gets up and finds a wallet lying with an address in it. He goes to return the wallet and meets its owner, a wheelchair-bound chess master named Pandit Omkar Nath Dhar (Amitabh Bachchan), who tells him he was Noorie's chess teacher. The Pandit starts teaching Daanish chess and tells him about his own late daughter Nina, who used to teach chess to Ruhi, the daughter of Welfare Minister Yazaad Qureshi (Manav Kaul). Nina mysteriously slipped down the stairs at Qureshi's house, dying on the spot. The Pandit is convinced this was not an accident but the police believe Qureshi's version of how Nina died. Daanish finds out that Qureshi and his daughter were the lone survivors of a terrorist attack on their village in Kashmir, after which Qureshi became a poster-boy for peace and a political force. Intrigued, Daanish goes to meet Qureshi, but meets senior Delhi police officers at Qureshi's office, who threaten Daanish with arrest if he troubles the minister. Daanish then tries to meet Ruhana at their house, but she refuses to let him in. He then goes to the Pandit's house and they play vodka-fuelled chess, during which Daanish finally beats the Pandit. The Pandit then meets Ruhana and tells her she should help his class of children complete a dance-drama that Nina wrote, for Noorie's sake. Daanish goes to meet Qureshi's daughter Ruhi at her school and goes through her sketchbook, in which there is a sketch of Nina. He asks Ruhi about where she was when Nina died, but Ruhi's minder takes her away.

Ruhana meets Daanish at the drama's rehearsal and the Pandit tells her how Daanish had almost committed suicide and how the Pandit himself had lost his wife in a driving accident, leaving him with no-one to share his grief when Nina died. Meanwhile, Qureshi threatens Ruhi for talking to Daanish, warning her to never do so again. The police close Nina's case file, despite the Pandit's protest. The Pandit awaits Qureshi's cavalcade and throws his shoe at Qureshi's car, breaking the minister's red beacon. That night, the Pandit is attacked by Wazir (Neil Nitin Mukesh), an assassin sent by Qureshi. Wazir brutally attacks Pandit with a knife and sets his wheelchair and chess set on fire. He also warns Pandit and Daanish to stop chasing Qureshi. Even more determined, Daanish persuades Sartaj to tap Qureshi's phone. As Qureshi travels to Kashmir, Wazir repeatedly phones Daanish and taunts him, pressuring him to stop Pandit from following Qureshi to Kashmir.

Daanish takes the Pandit to his home where the Pandit rekindles the love between Ruhaana and Daanish. However, the Pandit takes advantage of the opportunity and leaves the house quietly for the airport to travel to Kashmir. Wazir calls Daanish, tells him where the Pandit is heading and threatens to kill him. Daanish frantically chases the Pandit's van and eventually stops him. As he does so, Wazir blows up the Pandit's vehicle. Daanish is now determined to go to Kashmir, exact revenge from Qureshi and discover who Wazir is. He goes to Srinagar and meets the SP (John Abraham), with whom he plans to get to Qureshi during a speech. During the speech, the SP detonates explosives amongst Qureshi's supporters, causing panic. The SP then holds off commandos, giving Daanish time. Daanish chases Qureshi and eventually breaks into his room. He demands to know where Wazir is - Qureshi claims he doesn't know anybody called Wazir. Qureshi's daughter Ruhi emerges and confides to Daanish that Qureshi is not her father - he is actually one of the militants who massacred Ruhi's entire village and posed as her father (threatening her not to tell anybody) when Indian Army troops arrived to secure the village. Ruhi had told Nina this, so Qureshi killed Nina by pushing her down the stairs. Ruhi also tells Daanish that terrorists continued to meet Qureshi in Delhi. Daanish realises that Rameez had come to Delhi to meet Qureshi, and shoots Qureshi dead.

A few days later, while watching the Pandit's dance-drama enacted by kids, Daanish realises that the Pandit was in fact the play's 'weak pawn' who befriended a 'strong rook' (Daanish) who would kill a 'wicked king' (Qureshi). Daanish leaves and rushes to find the Pandit's housekeeper, Pammi, who say she didn't actually see Wazir on the night he supposedly attacked the Pandit. Pammi gives Daanish a USB stick fashioned out of a queen chess piece (which the Pandit had told her to give him if he came looking for 'Wazir'). On the USB is a video of the Pandit explaining what he did. Daanish realises that Wazir never existed and was just a persona made up by the Pandit, who knew he was powerless against Qureshi. The Pandit intentionally dropped his wallet near Noorie's grave, so Daanish could find it and then befriend him. All the Pandit's knife wounds were self-inflicted, and he had used voice recordings to pose as Wazir. The Pandit knew that he would have to sacrifice himself in order to ensure that Daanish would kill Qureshi and take revenge for both of them. Daanish and Ruhana are then reunited.