Keeping the horde of nanomachines at bay?

So… we have beings that are of spirit-material, and they produce nano-machines (which benefit their physiology)… which in turn can produce a particular “virus”.

It is not apparent to me why machine guns would work against spirit-material. I am going to infer that they are of physical material, and the “spirit” thing is… whatever. Actually, it might be preferable to have it that spirit material is as though it is physical material, in this respect. (Spirit material is mysterious, and gets to function in mysterious ways. (Also, at the time of writing, it is popular in shows to have human beings using physical-world mechanisms against spirit-type beings… although maybe not simply guns; maybe special guns that fire ammunition made of the right kind of material.) )

I am going to take it that the nano-machines and the virus are of the same material as the nature spirits.

This “virus” I have to take to actually be a virus — particularly, to rely on a host to reproduce, and, pertinently, to kill by reproducing.

(It does not immediately seem to fit, that this “virus” can influence [“recruit”] more complex organisms. Conversely, it is not a great stretch that, by the same token as it can improve their physiology, it can also influence their brain chemistry. In the case of the nano-machines, presumably both sides have been designed so that this works. Also hand-waving.)

I am going to infer that, like a normal virus, it does not survive long-term outside of a host. This gives us a reason why it survives in the “Dark Zone” — being a place where life can not survive — being that it can survive here long-term precisely because {whatever force it is that prevents it from surviving long-term} is absent.

I am thinking that this is up to the OP because it is somewhat constrained by the detail of the world. Otherwise… . We could take “Dark Zone” literally, and take it that there is no ultraviolet light, but that seems to be unsupported; the “Dark Zone” is dark metaphorically. However, there is no organic life in the dark zone, so we can take it that there are no threats to the virus as a result. I don’t think we really need to argue the point here; it seems reasonable without weird elaboration.

As for how the virus has been eradicated from the rest of the world — a vaccine. Presumably it has to be pretty sophisticated, to deal with such a sophisticated virus, but the notion seems quite plausible.

This has the benefit of leaving the virus free to exist temporarily outside of the body, to construct small attacks aganist villages and cities, before dying (as in, failing to survive long-term).

Presumably the slimes can support the virus [so that it does not die; possibly some minor reproduction without killing the host, at a stretch] but are not susceptible to it.

I originally took “creating monsters” to represent anomalously sophisticated behaviour by the virus. Alternatively… either • it can influence the “slimes” to go rabid, or • it can get the nano-machines to group together and function as a monster somehow.

I am not sure about the sieges. Perhaps the virus can get the slimes to sit near the target. Perhaps something more sophisticated is required. I think I shall leave this to the OP.

This seems to me to work, and to not be hugely contrived.

Living in Shadow

Nanotech has something of a reputation for being hard to kill and hard to contain. It's mostly unfounded.

Nanotech in reality is quite fragile and limited in capability. A swarm of nanomachines could feasibly disassemble a person, but once they did, UV radiation from the sun would quickly destroy most of them. Nanites are vulnerable to unusual heat, or cold, or radiation, acids, extreme chemistry in general.. They need a host, or a stable neutral environment at least.

This neatly explains why the nanoswarms opt to create/subvert living creatures in order to attack humanity. They can't survive long outside of an organic body

So the Nanites need a place where they can work, secure from UV radiation and possessing a decent population of animals to work with. Hence, the Dark Zone.
A dense forest with near complete coverage of its leafy canopy.
It's literally dark there, and anyone who goes into it has a good chance of never coming out, or coming out...changed..

Other Nanite holdouts exist, but most are far smaller, and lack the security of this one massive forest. Places where a lone wood-nymph is known to live aren't associated nearly as strongly with the nanomachines because they can't be as aggressive

Nanites can't create a stable communication mesh with each other, they need a controlling entity. However, these controlling entities can't be too close to each other or the individually very stupid nanobots get confused by which orders they should follow due to the relative signal strength being too similar. It's working fine inside the bodies of the spirits, because their bodies shield the nanites inside from outside signals, but, once the nanites leave their bodies, the conflicting signals cause increasingly erratic behavior the further they get away from the body.

Spirits don't have the signal strength to command outside nanites at a long range, so they have to build communication hubs every few kilometers to allow nanites to operate outside the bodies of spirits. Those hubs are fairly easy to build, once a spirit reaches a suitable place, since the nanites know how to build it and just need to be ordered to.

The Foundation managed to build their own rudimentary communication hubs that send a distortion signal which causes nanites to retreat or shut down if they get too close, but the signal isn't strong enough to disrupt nanites that are near an original communication hub. They still managed to establish a line of disruption hubs to set up the border to the dark zone.

The nanites switched over to building constructs which ignore all outside signals to try to take down the disruption hubs. If they manage to take one down, a spirit follows up and builds a new communication hub, expanding the dark zone. However, there are too few spirits to risk them, so they don't show themselves until an area has been completely secured by nanite constructs.

Some creatures have a natural shield against the disruption signals, so those creatures can carry nanites out of the dark zone, intentionally or not, which then follow their basic programming. Those wayward nanites are incapable of complex action due to their lack of communication.

Energy consumption

You state that the nanites gather energy for the spirits. That means these older nanites mightvstill be active all over the world, powering the new WMD swarm. This swarm was very successful due to this extra supply of energy, allowing more energetic nanomachines. However, they reached far outside their energy limit, unbeknownst to man. Man started winning battles, as the nanites couldn't function correctly with too littpe energy. The Foundation thought they had finally devised a way to beat them, but were halted when they finally beat enough nanites that the swarm had enough energy again. The swarm is now developing ways to go above this limit without needlessly taxing nature or the energy limit.

This standstill is the dark zone. Waiting. Biding time. Developing itself for another strike at humankind. The Foundation is keeping a minor spread at bay with it's own nanomachines and some enzymes and EMP, but can't beat the swarm any further. It is only a matter of time before the swarm tries again in earnest with a new strain of nanomachines.

Energy crisis

These nanites are designed to operate within organic beings, so they might primarily run themselves by drawing kinetic energy from the motion of fluids or chemical energy from nutrients. Only a limited number of nanites can run in a single body at once, else their energy requirements overtake the energy their host can provide, or their heat production kills the host rather messily.

Out in the world, they had to find another source of power for continent-spanning operations — perhaps nanite squadrons formed up to make big solar arrays, as the majority of the energy you can get out of the Earth is from solar influx.

The Foundation deployed massive quantities of aerosols or launched starshades into orbit to darken the sky and force the nanites to abandon their large-scale power systems, relying on local organic materials for energy instead. Your "Dark Zone" is called that because, thanks to some clever climate-manipulation tech, it's perpetually dark there.

The nanites use IPv6 for communication.

^{Source of the image above: https://xkcd.com/865/}

They are limited therefore to 2¹²⁸ bots operating at the same time. Any extra nanobots are unable to communicate with the network and self-destruct themselves.

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Edit: I love this comment:

You need to use IPv4. The Earth has a surface of 1.48 $times$ 10¹⁴m². That leaves you with about 2.9 $times$ 10²⁰ addresses per m². The human body has about 3 $times$ 10¹³ cells with a volume of ~62 liters. If nanobots are the size of an average human cell then you have enough addresses for a 600km deep grey goo to cover the whole globe using IPv6.

The nanobots can therefore further be constrained, as Nosajimiki suggests, by using IPv4, which will limit the maximum amount of nanobots to 2³². That is many orders of magnitude less bots and should make for a thinner layer of grey goo on the planet.

There is also this comment from the OP:

The solution is actually dumber. Warriors don't have a unique IP address, only a broadcast address. Generals can only communicate with them via broadcasts. It's dumb but it works.

^{(It's dumb but it works is also incidentally what I think about 90% of my most creative answers in this site).}

This allows for larger nanobot armies, but on the other hand also makes the army more vulnerable to IP spoofing. You only need to spoof one address in order to override control of a large number of nanobots. The constraint against nanobots in this case is that you can turn them against themselves much more easily.

You have not defined the nanites, which you should have done. Consequently, I'm making outrageous assumptions.

Assumptions: (a) Your nanites are synthetic, not biological,¹ (b) the purpose of the P-organ is to manufacture synthetic nanites.² (c) Your nanites are electrically based.³ (c) Your nanites are not capable of carrying an infinite supply of power.⁴

The nanites are capable of gathering energy — but the more dispersed they are the less efficiently they can gather and store the energy. Therefore, there is a minimum density of nanites required to produce "infinite" energy. This is important, because it means that together they stand and divided they fall.

The "Dark Zone" is a complex place. It's a 3-dimensional space constantly expanding and contracting based on the number of available nanites, the available energy to be gathered, and the strength of everyone else's attack. And what might that attack be?

An EMP leading to a Pinch.

A pinch is the compression of an electrically conducting filament by magnetic forces.

When the nanites are dispersed enough, a plain electromagnetic pulse (EMP) is enough to drop them like proverbial flies. You're probably eating some right now with your Wheaties. Little honkers are everywhere. Their corpses do tend to bond to tooth enamel, leading to a drop in dentist visits, but that's a really small silver lining (unless you're General Mills, then it's a big silver lining...).

Anyway, the closer you get to the Dark Zone the more an EMP isn't enough to keep them completely constrained. The heartless harpies keep getting out in bunches and garrotting unsuspecting lawyers and stealing everyone's left sock. And it's not like you can just go around setting off nuclear bombs or even synthesizing EMPs. People really do like to stream Netflix, you know!

That's where the Pinch comes in. Basically, the Dark Zone is encompassed on all sides by evil pinched plasma, which crushes the nanites down to the point of Critical Mass where there are so many nanites and enough accessible energy that they can produce a force against the pinch.⁵

At any rate, the solution does produce a lovely glow, somewhat purplish, not unlike an Aurora Borealis, and it tends to play Stevie Wonder's Superstition and OneRepublic's Secrets. It's driving us a bit batty, listening to the same two songs over and over under a purple glow (SPIDERS!) but it's a price worth paying to keep the nanites at bay!

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_{¹ Biological nanites are called "viruses."}

_{² Which is the Holy Grail of manufacturing. No employees, no robots, just a big Axolotl Tank churning out nanites and an IV tube for nutrients. OK, it's small and has blood vessels... Still....}

_{³ I though about using the weak/strong nuclear forces, but coming up with a gravity-wave generator seemed so much like Clarkean Magic that it made asking your question in the first place somewhat moot.}

_{⁴ Which is a requirement. There has to be a limitation of some kind. Limitations and weaknesses are what make stories believable. A nanite with an infinite power source is basically unstoppable.}

_{⁵ Or replicate fast enough that it doesn't matter. We're not completely sure which. It takes a lot of nanites to build up what we might call "dirt" to a large enough degree that we can tell they're dying by the septillions behind the pinch.}

No matter how complex or what materials they are made off, in the end your WMD nanites will take the form of a type of biological conglomeration of virusses ranging up to bacteria to do its job. You already mentioned that these have a type of collective intelligence, being able to discern human from other biologicals and spirits as well as discerning distress and having the ability to think off how to act on that. We can use that.

The Dark Zone was a first successful attempt at stopping the nanites. For convenience lets say it was a geniusly created nanite swarm designed to combat the opposing nanites and nothing more. Maybe it comandeers the WMD nanites to fight for it or it eats WMD nanites, either way the WMD nanites learned to avoid them.

The thing is that if you can create a Dark Zone, you can start moving that Dark Zone until the WMD nanites are destroyed. So for whatever reason the creator of the Dark Zone and the devices he used were destroyed in the first attacks made by the nanite swarm (or one of the opposing facrions who had no idea/feared the technology) and a deadly staring contest began: the WMD nanites think that crossing the Dark Zone without a host is suicide, the 3 other factions can only try to maintain that idea so that the WMD nanites stay put.

You can use variations of this idea with similar results. The Dark Zone is a bunch of buildings that they dont have the resources to move or build more off, the buildings influencing the WMD nanites thoughts so they stop and turn back. Or the resources required to move the Dark Zone on your end means the other factions can defeat you etc.

Anti-nanites:

I know very little about the relative tech of the humans and Foundation, but I get the impression the foundation is high-tech and is trying to be neutral - or they are anti-WMD. So the Foundation creates anti-nanites who's sole function is to destroy the WMD nanites. The planet is already nano-contaminated, so there's no ethics problems using this "bad" technology. Since anti-nanites strip the nanites down and reuse the parts, it takes less to convert a nanite to an anti-nanite than it does to build a nanite from scratch.

The nature/WMD nano-horde is semi-self aware, and organized enough to secure it's home base against anti-nanites. The "beasts" it creates are either programmed non-nanite animals, or else functionally packets of nanites secured in a nanite-resistant shell sent to venture out to attack. Too many of them, or if they go too far for too long, and the anti-nanites show up and kill the nano-beasts.

Humans are good with old-fashioned tech, like guns and bombs, making it quite practical to build weapons that can oppose glorified giant animals. I'm guessing, though, that the Foundation isn't too happy with humans pillaging the planet and slaughtering the natives. Or maybe the Foundation ethically CAN'T kill humans, despite the fact they really want the humans gone so they can sterilize the planet to get rid of the nanites. The nano-horde either isn't strong enough to defeat the Foundation, or doesn't recognize them as an allowable target (since they don't threaten the environment). Since the Foundation hates nano-weapons but dislikes the actions of the humans, they don't cooperate or actively oppose/withdraw protection when humans are getting too invasive.

The foundation can't get rid of the nanites and are too honorable/rule-bound to get rid of the humans. The humans need the Foundation to protect them from being wiped out, but can only contain the nanites. The nano-horde can't defeat the anti-nanites, and are stymied in their efforts to wipe out humans.

Three-way stasis with constant conflict.

Why do you need reason to force it to use organic constructs?

Just write it so that the nanomachines are of the Von Neumann variety but not the grey goo variety, like in Day After Tommorrow.

Or make them so they are unable to self-replicate in which case they can only be produced by P-organs and therefore can must manipulate their surroundings like anything else by either building or taking control of organic bodies.

The nanovirus can be hacked

Since the foundation has figured out how to hack their communications signals, they can purge the homicidal nature from the infected nanites just by getting close to it with a wireless device. So, it is just as dangerous for the bots to go into a city full of routers and cellphones as it is for man to go into an undeveloped forest, because the humans can purge them anywhere they can bring an internet connection.

But, hacking the nanobots requires breaking an encryption key in real time. As we know in the modern age, that is easier said than done, but if the Foundation has stable quantum computers, then they could. If your phone detects the presence of nanites, it transmits the communications patterns of the nanites to one of the quantum computing stations where it is cracked, and the kill code returned to the phone to be transmitted moments latter.

This is why the border is so hard for either faction to move without really fighting for it, anywhere humans already have an internet connection, we can repel the virus, but if we get too far from a physical connection, we lose signal and the virus can swarm us. Humans are constantly trying to expand our internet coverage, but nanites have learned to jam our satellite communication by blacking out the skies over the Dark Zone well enough to force us to use a physical network of actual wires and stuff; so, the war is a constant push for humans to expand our networks into the wild places of the Earth while the nanovirus monsters are sent out to destroy our networks allowing the virus to expand the Dark Zone.