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.

Pathaan, a RAW agent, and his senior officer Nandini Grewal, 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. With Colonel Sunil Luthra’s permission, Pathaan and his team head to Dubai to stop Outfit X’s suspected plans of attacking the President of India. However, they realise that their actual plan was to kidnap two scientists, Dr. Farooqui and Dr. Sahani.

Jim, who leads Outfit X, attacks the scientists’ convoy and Pathaan tries to stop him. A fight ensues where Jim manages to escape with Dr. Sahani. Luthra reveals that Jim was a former agent and Kabir’s former partner, who was awarded the Vir Puraskar for his bravery after the agency could not find his body when Somalian terrorists kidnapped him and killed his pregnant wife out of vengeance for a ransom deal gone wrong. He faked his death in order to seek vengeance against the country.