NPCs are not soulless automatons

NPCs are egregore-controlled humans, they still have an independent mind but their mind is enslaved and used as a tool for expressing the egregore mind, like a two-way radio channel.
see https://en.wikipedia.org/wiki/Egregore
Its possible to disrupt the link to egregore by subversive thought insertion(aka memes), allowing the original mind to assert its will and independent thought. The egregore can't focus on multiple mental challenges simultaneously and the "radio channel" has limited capacity.
NPCs can be reformed to PCs.

when NPCs wake up

Within a period of forty to fifty years at the end of the thirteenth and the beginning of the twelfth century almost every significant city in the eastern Mediterranean world was destroyed, many of them never to be occupied again.[5] https://en.wikipedia.org/wiki/Late_Bronze_Age_collapse