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For almost as long as I've been running tabletop campaigns, I've had the idea of running combat against a monster so big that even Colossal is too small to properly encapsulate it (though, honestly, I feel like Colossal monsters are already big enough that you could probably run them this way). Of course, I've always had the vague notion of running it as essentially terrain or a small dungeon with its various limbs and the like basically functioning as monsters, traps, or other hazards, themselves, but I'm wondering if anyone else has actually taken a stab at this sort of thing, or perhaps even if there's been some supplement that details a strategy for it.
(Incidentally, the earliest envisioning of this idea was for an apocalyptic Eberron campaign particularly inspired by the kaorti. It would eventually culminate in the PCs traveling to the Far Realm and having to fight creatures that I described as being of unfathomable size and alien dimensions such that many could be as incomprehensible to the PCs of even be creatures as the PCs would be unnoticeable to them, swimming through a multidimensional space that would cause them to even appear to be crawling through each other. Amusingly, despite this being the mid-2000s and so before Pathfinder even got off the ground, my imagination mostly rendered these things as pretty much city-sized keketar.)

blahpers |

At that scale--well beyond the scale of kaiju being climbable by Huge or smaller creatures--I'd just treat the "creature" as a living dungeon.
Human-sized creatures already have microbiomes; they're just too small for creatures of similar size to notice. Any creature large enough to be terrain for a human no longer has a microbiome--it has a biome, an entire ecosystem, as far as human-sized PCs are concerned. Such an ecosystem has different areas of terrain in different parts of the creature as well as flora and fauna "small" enough to be unnoticed and/or in symbiotic or parasitic relationships with the host creature.
The challenges would present themselves at a scale the party could understand--like breaking into the creature through a shielded vent hole or something, then traveling through the creature's interior to reach the beast's core/heart/brain or something, fighting off dragon-sized lymphocytes, parleying with poor souls swallowed alive when the beast ate their town, and so on.

EldonGuyre |
Yup, been there, done that. One of the final fights in my last campaign - a mythic game - involved a fight inside a creature so large that the fight was actually in its mouth, against independent entities it created to act as digestion agents...
...this happened in the Far Realms.
There are island turtles in my upcoming game.