In October 1999 in London, a teenage Zoya witnesses her father, ISI agent Rehan Nazar, die in a bomb blast. After his funeral, Zoya is visited by Nazar's protege Aatish Rehman, who persuades her to join the ISI.

In the present, Avinash "Tiger" Singh Rathore is assigned by the new RAW chief Maithili Menon, to rescue Tiger's former aid, Gopi Arya, who was captured during a mission in Afghanistan while trying to extract information from the Taliban about a mission being planned in Pakistan. Following his rescue, Gopi reveals to Tiger that his wife Zoya is a double agent working for them, and is involved in the mission, before succumbing to his injuries. Tiger begins to spy on Zoya and is later assigned by Menon to safeguard an arms supplier, Jibran Sheikh in St. Petersburg, Russia, who worked with Gopi and escaped to the country after being discovered in Pakistan. Tiger witnesses Zoya's attempt to assassinate Sheikh; after saving him, Tiger is captured by Aatish, who reveals that he forced Zoya to assassinate Sheikh by near-fatally drugging and kidnapping her and Tiger's son Junior.

In a flashback, twelve years prior, in 2011, one year before the events of Ek Tha Tiger, Aatish sought to derail a peace treaty between India and Pakistan in Vienna by assassinating the Indian Army Chief, General Ribeiro. Aatish tasked Zoya with the job, but she refused to cooperate and covertly informed the Indian consulate, where, unknown to her, the message was received by Tiger, who didn't know her back then. Aatish's pregnant wife Shaheen Baig decided to assassinate the general herself, but was shot and killed by Tiger. Aatish denied that his agents knew about the plan, leading to his imprisonment and ousting from the ISI.

Tiger and Zoya recruit their team, consisting of Rakesh, Karan and newbie Nikhil, to steal a briefcase for Aatish, containing missile launch codes in Istanbul in exchange for Junior. However, Aatish has Tiger and Zoya framed as traitors by their respective countries, despite releasing Junior, leading to Tiger's imprisonment at a military prison in Northern Pakistan. Tiger is sentenced to death, but manages to escape with the help of Pathaan.

Tiger hides in Islamabad and meets his adopted son Hassan. Tiger's team, Zoya and ISI agents Abrar and Javed return to Islamabad, where they learn that Aatish and General Imtiaz Haq, the Army Chief of Pakistan, are planning to assassinate the Prime Minister of Pakistan Nasreen Irani in order for Aatish to replace her. Seeking to save Irani, Tiger, Zoya and their team secretly enter Pakistan's PMO and expose Aatish's plan to Irani. Tiger and Zoya escort Irani to an underground bunker of Pakistan's PMO and Tiger forces General Haq to publicly reveal the plan.

However, Aatish secretly kills General Haq with the help of Javed, who shockingly betrays Karan and Abrar by killing them. After they locate Irani, Hassan sacrifices himself, allowing Tiger and Zoya to help Irani escape; in the process, Tiger reveals to Aatish he knew about Javed's defection, having discovered his identity as Shaheen's brother. Zoya avenges Abrar and Karan's deaths by killing Javed. A fight ensues between Tiger and Aatish, ending with Tiger killing Aatish. Irani exposes Aatish's plot to the public. Tiger, Zoya and t…

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