Plot
In 2019, the Indian Government revokes Article 370 of the Indian Constitution, which grants special status for Jammu and Kashmir. The news impacts a cancer-ridden Pakistani Army officer, General Qadir, who decides to exact vengeance against India and signs a contract with a private terrorist organisation called Outfit X.
2022: Pathaan, a RAW agent, travels to Africa and captures arms dealer Raafe. Back in India, upon inquisition by a junior, RAW officer Nandini Grewal narrates Pathaan's past after something they have been looking for is found.
2020: Shortly after recovering from a mission in Myanmar, Pathaan and Nandini form a unit known as "Joint Operations and Covert Research" (J.O.C.R.) to recruit ex-agents and soldiers who were forced to retire, but want to continue serving their country. Outfit X's actual plan was to kidnap two scientists, Dr. Farooqui and Dr. Sahani, who were initially supposed to be part of the President's convoy.
Jim, who is gang leads Outfit X, attacks the scientists' convoy and Pathaan tries to stop him. A fight ensues and Jim manages to escape with Dr. Sahani. During a debrief back at agency headquarters, Luthra reveals to Pathaan and Nandini that Jim was a former agent and Kabir's former partner, who was awarded the Vir Puraskar posthumously.
Meanwhile, he is made aware of a codeword, "Raktbeej", in the process, he learns that the dead people in Dubai were ex-agents and their money was transferred from the account of Rubina "Rubai" Mohsin, a Pakistani doctor in Spain. He travels to Spain and is captured by Jim's men, all former agents of their respective national intelligence agencies, where he also learns that Rubai is an ex-ISI agent, and Raafe his henchman. When Jim leaves his hideout, Rubai attacks Jim's men and escapes with him. Following a nightmare about her childhood wherein her father, a doctor, was forcibly tortured to death, Rubai reveals that Raktbeej is in Moscow, and they travel to steal it before Jim does. Almost on the verge of the mission being successful, Rubai betrays him and has him captured by the Russian police. It is revealed that Jim used Rubai to trick him into stealing the Raktbeej for himself. After Nandini disclaims him, he is taken to prison by a train, but is saved by Tiger.
2022: Pathaan meets Nandini and reveals that Jim is purchasing two Saber missiles, while Nandini reveals Rubai's location in Paris. He meets Rubai, who reveals that "Raktbeej" is codeword for a mutated smallpox virus, which was forcibly developed by a captive Dr. Sahani under Jim's orders. They travel to Jim's lab in Siberia and manage to recover one orb containing the virus, while Jim escapes with the other orb. Luthra and Nandini reach Jim's lab to take the orb back to India in order to develop a vaccine.
At the Indian Institute of Contagious Diseases, Dr. Farooqui opens up the orb to Nandini without apparently finding anything. Jim calls them and reveals that the orb has already spread the virus in the facility. Later, the facility is destroyed in a controlled blast. Jim provides an ultimatum to evacuate Indian soldiers out of Kashmir within 24 hours. He 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 after he activates the missile. 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.
Rubai informs Pathaan, who finds that Jim has the detonator. Luthra calls the air traffic control to prevent the plane from landing in Delhi. Crashing into a cabin after a long chase mid-air, Pathaan and Jim fight brutally. This enrages Pathaan steals the detonator, deactivates Raktbeej, and kills Jim. Afterward, he is reinstated and made the head of J.O.C.R., with Luthra giving him a file of soldiers who were also forced to retire but want to continue serving the country for Pathaan to program mentor and train them, while Nandini is posthumously awarded with the Vir Puraskar for her bravery.
During a mind-credits scene, harking back to their interaction, Pathaan and Tiger are brother seen pondering about retiring and suggesting young agents who can help replaces them, but eventually decided to keep fighting the threats themselves.
