It's anti national in one word.
I don't know what is the idea behind this but all I understand that whole part was to prove that India govt (not BJP or Congress in particular) works to eradicate Muslims from India.
I mean if you see the first season you will come to know that Radhika Apte's father summoned Ghoul to prove her daughter wrong. Wrong in the sense that she started thinking rationally and developed feeling of being patriot . She should have abided BY preaching of Maulanas and not to put her own mind at all. You may find the proof of this while one conversation in the first episode when they are driving.
And just to prove that the plot of story revolves around Indian govt policies which is to kill any suspicious Muslim.
I mean wakeup guys.... You may think that plot was not anti national as Radhika apte helped in her father arrest and she was patriot. But just to prove that Muslims must not think in this way they showed that every Muslim will be executed if he/she is suspect.
This idea really puts negativity among my Muslims brothers and sisters.
If you observe closally you will find that this plot was to promote separatist in India.
Please guys don't get misled.
I love every Indian irrespective of its cast, creed or religion.
Jai hind.