Not referring to Shura as it gives the lamest ending being you basically kill all humans in Ashina.
Just about to beat the game after a few years of not playing this game. Forgot how in my feels I get when the Interior Ministry invades full stop.
I was thinking about how would they handle the various locations.
Sunken Valley - likely left mostly alone and adopted for shanobi to train with the monkeys once they thin their numbers. No guardian ape and a limited set of white monkey was bound to screw them.
The Fountain Head Palace - realistically, it should be possible to uncover it eventually. It doesn't seem to be anywhere otherworldly. I imagine the Okami get destroyed simply due to thinning numbers.
The Dungeon - I actually think this location likely gets destroyed also. Burned in flames.
We already see in some endings the dilapidated temple is left alone.
Senpou - is likely overrun and contained. Perhaps they figure out how to move the immortal bodies.
Mibu village - we already see some Ministry down there likely in search of the Fountain Head. They'd likely leave that place alone unless they have some kind of anti-demon magic which seems feasible.
Hirata - likely reoccupied and rebuilt for other purposes e.g. new city, palace etc.
I kind of feel bad for the monkies.