You’ll have to forgive me for some time until my lovecraftian fever wears down, but for now I’m so up for this.
So in the Whisperer In The Darkness, the story where the MiGos appear (if you haven’t read it and are interested, do yourself a favor and read it, it’s VERY GOOD) they live in the hills, hidden in caves, where they are miners searching for stuff they don’t have in their planet.
They are really obsessed with hiding and not be seen at all, and they live in communities.
What about having a kinda mid level dungeon or even an special kind of mine that is infested with them? With ore loot or maybe some strange bionics -they were very good at that.
I don’t think it could be some kind of overlap thing like a fungal tower, that would mean the end of low level players, but hiding in caves could work!