| Coidzor |
I suppose you could approach it as the giant monster *being* the dungeon and as you progress inside you fight various parts of its immune system and then finally its "heart" or "core" or actual literal heart. Like Lavos from Chrono Trigger.
That'd probably be the quickest and dirtiest way to approach it.
I don't think there's a good way to model Shadow of the Colossus style combats in Pathfinder, but I may be forgetting something there.