Pathaan is essentially a cyberwarfare done by the ISI/Pakistan in order to stir up pro Pak sympathy in india.
In one of the later scenes the female ISI agent (played by padukone) explains that she turns on the Pakis/Villain because the plan to attack India w a bioweapon was "formulated by extremists who have taken over ISI" and in another scene she explains how "the regular pakistani folk would hang the general for such a ruthless and barbaric attack".
It seems as if bollywood has zero understanding of the history of the insurgency in J and K, and how ISI trained militants behaved with hindu civilians. Moreover, the average Pakistani, leftists and rightists alike, support the killing of our jawans, pandits, and destruction of india. Fact is we are not at war with any "extremists" in Pak. We are at war with their whole state.
How such propaganda in india can be tolerated by the government shows the seriousness of india as a nation.