Story line:

2019 article 370 is withdrawn by Indian government in Jammu Kashmir.Pakistani General Qadir along with a terrorist Jim decides to plan a big attack on India.In present times Pathaan a RAW agent is traced in Africa who was missing since years his senior officer Nandini comes across suspicious activity and decides to trace Pathaan Back to the past Pathaan had started the JOCR (Joint Operation and Covert Research) which recruited soldiers with disability and trauma and was headed by Nandini. Their first mission is to stop Jim from kidnapping the Indian president in Dubai but Jim has other plans and kidnaps a scientist, Dr Sahani. Pathaan learns that Jim was a former RAW agent who was disowned by the country and now wants to revenge his humiliation after loosing his family. Pathaan traces Dr Rubina Mohsin in Spain who can lead him to Jim. She turns out to be his mole but Rubina saves Pathaan and revels her true identify of being an ISI agent. Rubina discloses to Pathaan that Jim is behind Rakhtbheej which can cause destruction and is in Russia and to stop Jim they have to team up. Pathaan and Rubina get hold of Rakhtbheej but Rubina deceives Pathaan and leaves him to die at the mercy of Russian government.