In 2019, the Indian Government revokes Article 370, which grants special status for Jammu and Kashmir. The news impacts a cancer-ridden Pakistani army general, Qadir (Manish Wadhwa), who decides to exact vengeance against India. The doctors have given him 3 yrs to live. He signs a contract with Jim (John Abraham), who leads "Outfit X", a private terrorist organization. Meanwhile, Pathaan (Shah Rukh Khan), a former RAW agent, and his senior officer Nandini Grewal (Dimple Kapadia) open a unit dubbed the "Joint Operations and Covert Research" (JOCR) unit, to recruit former RAW agents who were forced to retire due to past trauma or injury, but want to serve the country. Pathaan was injured in an operation in Myanmar and has metal plates in his foot and neck and screws in his shoulders to hold his body together. JCOR includes: Shweta Bajaj (Ekta Kaul), hacker. Raza (Shaji Choudhary). Joseph Mathews (Diganta Hazarika), sniper. Amol (Aakash Bhatija). Rishi Arya (Viraf Patel), intelligence analyst.With RAW joint secretary, Colonel Sunil Luthra's (Ashutosh Rana) acceptance (Pathaan convinces him that Outfit X has its hands in all the major terrorist attacks of the last decade), Pathaan and his team head to Dubai to stop Outfit X's plans of attacking the President of India at a scientific conference. However, they realize that their actual plan was to kidnap two scientists, Dr. Farooqui (Prem Jhangiani) and Dr. Sahani (Prakash Belawadi) instead and the information they received about the imminent attack on the President was a ruse to mislead them. The Indian agencies increased the security for the President and reduced it for the scientists. Pathaan goes for the scientists. Jim attacks the scientists' convoy and Pathaan tries to stop him. A fight ensues (in which Rishi dies), where Jim manages to escape with Dr. Sahani. At the debrief back at the agency, Luthra reveals that Jim was a former RAW agent and Kabir Dhaliwal's partner. Jim was awarded with the Vir Puraskar for his bravery after the agency could not find his body when Somalian terrorists killed his wife and unborn child (Jim had extracted 6 hostages from the terrorists. The terrorists kidnapped him and his wife and wanted 10 crores for their release, which the Govt refused to pay). He had apparently faked his death in order to seek vengeance against the agency and country for not saving his family.Meanwhile, Pathaan learns about the code-word dubbed "Raktbeej" and also that the dead people in Dubai were ex-agents and their money was transferred from the account of Rubina "Rubai" Mohsin (Deepika Padukone), a Pakistani doctor in Spain. He travels to Spain and is captured by Jim's men, where he also learns that Rubai is an ex-ISI agent who works for JIm. Jim wants to recruit Pathaan into the Outfit X, but he refuses. Jim argues that they work on choice assignments and are paid handsomely. When Jim leaves his hideout, Rubai attacks Jim's men and escapes with Pathaan. Rubai is hit in the abdomen and Pathaan saves her. Rubai reveals that Raktbeej is in Moscow (Nandini advises against going after Raktbeej as they don't know what it is. and Russia is a friendly country and an all), where they travel to steal it before Jim does. The raktbeej is stored in the world's most secure vault with elaborate security measures. They fall in love with each other, trading stories of their past and how they came into the spy profession. Pathaan devices a plan to break into the vault and succeeds. However, Rubai betrays Pathaan and has him captured by the Russian police who converge at the vault, as Rubai escapes with the Raktbeej. It is revealed that Jim used Rubai to make Pathaan steal the Raktbeej for himself. Pathaan is captured (& tortured brutally) (Nandini tells the Russians that Pathaan is a rogue agent and his actions were not sanctioned by the Govt of India) and taken to prison by train, but is saved by Avinash "Tiger" Singh Rathore (Salman Khan).Three years later, Pathaan travels to Africa and captures Jim's henchman Raafe (Rajat Kaul). He is tracking Rubai. Pathaan abducts Raafe from an arms market and flies off in an helicopter after a brutal fight with the arm seller. Pathaan meets Nandini and reveals about Jim purchasing two saber missiles, while Nandini reveals Rubai's location in Paris (the JCOR facial recognition software identified her roaming the streets of Paris). Pathaan meets Rubai (he knows that Rubai being tracked JOCR was an invitation by Rubai for a meeting), who reveals that the Raktbeej is a mutated smallpox virus (the current vaccines don't work against it), which was forcibly developed by a captive Dr. Sahani under Jim's orders. She also expresses guilt about betraying Pathaan without knowing that her country would plan such an heinous attack (she reveals Gen Qadir was paying Jim). The virus is effective only for a few hrs and thus no risk of global contagion. It will only devastate Indian cities against which it will be launched via missiles. They travel to Jim's lab in Siberia (They cannot destroy it with missiles as virus could escape and travel via could to 3 continents) and manage to recover one orb containing the virus with great difficulty, while Jim escapes with the other orb. Luthra and Nandini reach Jim's lab to take the orb back to the Indian Institute of Contagious Diseases (IICD), in India in order to develop a vaccine. Luthra also has Rubai arrested for having questionable loyalties.At the IICD in India, Dr. Farooqui demonstrates the orb to Nandini. Jim calls them and reveals that the orb has already spread the virus in the facility. The infected scientists, along with Nandini die in the facility by shooting themselves, to curb the spread of the virus. Later, the facility is destroyed in a controlled blast. Jim provides an ultimatum to evacuate Indian soldiers out of Kashmir within 24 hours else he will launch the virus against an Indian city via his missile. Pathaan interrogates Raafe about the location of the missile, and learns that the missile is situated in Afghanistan. After rescuing Rubai, they lure Jim's associates into a trap, and attack Jim's base. Qadir is killed by Rubai before activating the missile containing the virus. Pathaan chases after Jim with a jet-pack and they both crash land into a cabin.Meanwhile, Rubai deactivates the missile, but finds that Raktbeej is not in the missile, but instead in a passenger-bound airplane, which is about to land in Delhi. She informs Pathaan, who finds that Jim has the detonator. Luthra calls the air traffic control to prevent the plane from landing in Delhi. In the cabin, Pathaan and Jim fight brutally, resulting in the cabin begin sliding off a cliff. Despite getting stabbed by Jim, Pathaan steals the detonator, deactivates Raktbeej and throws Jim out of the cabin as the foundation is about to break. While Jim holds onto a plank, Pathaan takes away his Vir Puraskar, deeming him unworthy of it. He stomps and breaks the plank Jim was holding onto, resulting in him falling to his apparent death. Afterwards, Pathaan is reinstated into RAW and made as the head of JOCR, while Nandini is posthumously awarded with the Vir Puraskar for her bravery.In a mid-credits scene, Pathaan and Tiger are seen pondering about retiring and suggesting young agents who can replace them, but eventually decide to keep fighting the threats themselves.