to have a properly multilevel undercity you need distinct reasons for each layer i think
- cthonic temples of a vanished civilization cut into the living rock beneath one of their cities
- that city passes out of habitation and memory, a middle civilization builds atop it
- nearby river changes course, flooding buries the low-lying parts of that city
- rebuilt with lots of hydraulic infrastructure
- canals and stream sewers of that city are vaulted over and the current city built on top
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