The story is simple.
BJP thought demand of NRC in Assam was based on anti-Muslim threat but in reality the primitive Assamese people actually wanted to overcome the Bengali dominance over their state.
BJP's propaganda backfired and Bengali Hindus, the main BJP voteback in Assam, got declared illegals. BJP realized that this could happen during the listing process and suggested a new scheme to counter it called Citizenship Amendment Bill, which drew huge public outcry in the Northeast.
When Mamta said NRC could lead to civil war it wasn't based on hot air. Bengalis are the most scattered ethnic group in India, more like the Kurds in the former Ottoman Empire. You will find Bengali pockets in almost every state in India. If they start the NRC process throughout India, millions of Bengalis would be on the verge of being stateless, just like what happened in Assam. And passing Citizenship Bill will just rejuvenate the separatist movements in Northeast in a far more violent manner.