I know it is late, but:
- Are there any humans left on Earth? Can any spires meet them? Do the humans even speak the same language? Are there new kinds of humans after a 1000 years?
- How does the cave provide an ecosystem? I mean, plants need sunlight to process the stuff they eat into plant matter. Is it heat? I have read that thermosynthesis (using heat instead of sunlight) is real thing. Is the cave unique somehow, and is thus able to feed so many sentient creatures, or maybe that is the The Machine's function, to provide heat and energy into the cavern's ecosystem so it may live?
- Does that tail that realized that human "glyphs" are actually letters for sounds ever gain traction among the Internets? Or does the naiveness and own echo-chamber effect (the Internets believed them to be glyphs for so long that they refuse to consider it otherwise) prevent the idea from ever gaining ground?
- This is a more minor question, but DO the spires and fairies and whatnot have a writing system? I mean, there are names on memorials and graves and stuff. Maybe those are based on glyphs and thus the Internet's conviction that humans used glyphs?
- Is the underground system somehow closed-off or can it connect to other, different cave systems? With new people, believing different things?
- How come there are still so many robots around the cave system? Can't the native inhabitants get rid of them? I know that there was that one person who tried to capture a robot for the Internets to study, but I am talking about organized efforts and stuff like crushing them under big rocks or something. Plus, surely, some would recognize that the "banned" weapons would be best used against them, these robots that attack everyone and anyone?
- What DID happen during the Great War or whatever? There is argument whether humans done it or not, but neither has considered a third option: it was humans vs something else. Aliens? Or even against their new "cousins" of spires, tails and fairies? Or even a new species that gone extinct during the war?
- The ball woke up somehow in the lab. Is there a reason for that? Is it the ball from WaDF or is it a different ball altogether?
- What will be of Mi and her ball-shape biology thing? Won't it cause side-effects down the rode? What WAS that tube thing and how did it survive and be active for over a thousand years?
Oh, and as for radiation, there are few real things she could do:
1. Wear a gasmask. A relatively less-known danger of radioisotopes isn't just being near them (and being near them for an extend time), but swallowing them or breathing them in. It is far from a complete protection, however and does not prevent radioisotopes getting in other ways.
2. She has to fulfill biological functions, so special, sealed equipment for that would be needed. Most of all, she'd need some kind of shelter where she can sleep, eat/drink and yes, have a toilet. For something compact that she could carry on her person, the best I can imagine is some kind of futuristic, military NBC (Nuclear, biological, chemical) tent that has its own decontamination chamber, toiletry thingy and air-filter.
3. A hazmat suit. This is likely to be unnecessary for the surface, but let me detail it anyway. These hermetically-sealed suits incorporate a complete suit and gasmask like above, but also has metal lining to decrease incoming electromagnetic (ultraviolet, x-ray, gamma or even cosmic) radiation (IF it is a specialized radiation-hazard suit, other suits most likely would not have this). Current physics say that only dense material, like tungsten or lead can do this job. However, since this is fiction, you could make up special, powered suits that make some kind of forcefield around the wearer that would protect her from such radiation.
But in reality, after a 1000 years, only the first option would be PERHAPS necessary and even that only to be on the safe side. More likely, she'll need good desert-clothing, something to protect her from sunburn, keep her as cool as clothing would allow and keep herself dust-free.
The thing is, under a 1000 years, most radiation by-products would have degraded into either stable (non-radioactive) elements or into ones that have massive, million-year (or even more) half-lifes and thus produce only negligible amount of radiation. The second kind of element is much more common than people assume, and would be almost surely be present in any cave system (just living in concrete or rock house gives you extremely slight doses).