The setting is a homeworld exoplanet of an alien species, abandonded (save a hibernation cycle-style subterrainian research settlement) for conservation after a 10 000+ year prior climate collapse. this setting is part of most of my questions on this site. The story takes place roughly 60-70 years into a collapsing human settlement, and shortly after the aliens (for the purpose of clarity, I'm aware the humans are the aliens in this situation) wake up and announce themselves, a war breaks out.
The humans are mostly scatered and starved of resources, mostly due to past civilization on the planet using non-renuables, with a population of probably a little over 100 million over a small area, wrapped around a large river delta. The capital boasts a large military force, with basic and expensive hover tech and advanced projectile based weaponry. They figured out interplanetary space travel, but they got to the new planet via a natural, Sol-adjacent wormhole, so not technically interstellar tech level.
The native race has a very small population of mostly scientists, low infrastructure, and advanced tech (including energy-efficient low-altitude flight and advanced genetic engineering). Almost all their tech is made of bio-organic machines, including vehicles and service machines/animals. This biotech seemlessly incorporates metal alloys and other materials in a way that allows machines to be grown, bred and even consumed by other machines to recycle material.
Nano storm weapon:
Long preface, I know, but I introduce the tech because the setting makes me think the best idea the native city could use to defend is to make a lot of simple, small machines, able to be controlled by a small team of operators. These nano machines would work as you have probably seen in other scifi, a semi-hive mind storm of low-cognition units that can be allocated large/complex tasks.
Each machine would be able to break down and alter both organic and in-organic stuctures. With a quick enough strike, small team of nano-storms could disarm and dismantle a decent armada of tanks and infantry in a few hours with miniscule sentient loss of life, provided the operators only dismantle equipment and not soldiers.
This kind of tech is well within the range of my native race, but this is a story, and I can't just have the human threat be annihilated so quickly. How would a human army defend against such a weapon? What kind of counter-weapon might near-future tech provide?
Keep in mind he AI of these machines is organic, neuron-based, so Independence Day computer virus isn't gonna cut it. Also, i'm aware this may be too vague, but since it's been a bit of a hole in my writing for a while I felt the need to ask.