So, there are three major powers in the setting that can be reasoned with, and a fourth that is just there to destroy. I have a problem with balancing them.
The so-called nature spirits are creatures that, through one way or another, got a P-organ. P-organs are capable of manufacturing nano and micromachines to assist their hosts.
For nature spirits, this causes gigantism, a more efficient metabolism, sapience, increased lifespan, and modifications to the physiology when necessary, such as scaling a giant eagle's wings and flight muscles to allow for powered flight. These nanites are present in nature as well, giving their gathered energy to the nature spirits.
The problems start when humans begin to drive the nature spirits out of their habitats with their advanced firearms, killing those who resisted. Humans had an easy time since nature spirits are limited in number and aren't adequate to deal with things like .50 cal sniper rifles or tanks.
The turning point came, however, when the nanites sensed their hosts' overwhelming despair and identified the source as humanity. They only knew one Solution that could be Final for this problem:
Eradicating mankind with a nanovirus
This is where our problems start. You see, this nanovirus was an ancient WMD, designed to make entire continents yield. What's worse is that this virus has the ability to "recruit" living nature spirits and ambient nanites into its ranks, giving it access to the planet-wide energy harvesting system of the nanites.
Such a virus would crush humanity with little effort, but that isn't what happed.
In the story, the Foundation (the third party) manages to "restrict" the virus into the "Dark Zone" (as in you're dead if you enter), but can't hope to eradicate it.
For the most part, it sits around the place, creating monsters and unleashing them upon villages and sometimes cities. On rare occasions, it might stage large sieges which require a considerable military force to suppress. The infectious part is now only present in the Dark Zone and several monsters, most notably, slimes.
But how? What kind of weapon/tech would actually be able to stall this virus and force it to rely on organic robots, instead of infecting everyone?
The technological level of humanity is near-future, but the suppressing technology that keeps the nanites at bay can be much more complex, as long as it is scientifically plausible.