I'm wondering how to handle a massive dungeon environment.

In our homemade campaign setting, the campaign takes place in The Vale of Thorns, a nation-sized briar patch with a mean streak a countryside wide, with several isolated city states and vilalges that try to eke out an existence in this hostile rosebush.

The thing is, the entire Vale rests atop a massive ruined city, that is now infested with undead. It's generally intended for the players to make short forays into this place, known as the Labyrinth, to get from one place to another, or just fight undead. The thing is, this place is a nation-sized city. How can one make that work? And so it's clear, it wasn't underground when it was still habitable. Some cataclysm buried the city before the Thorns grew.

Is something like our Labyrinth even logically possible?