Sometimes a picture is worth a thousand words, and this picture by Börkur Eiríksson sums up a lot of the ideas I had for the megadungeon. Börkur's fan art of a forgotten beast from the game Dwarf Fortress shows an unknown threat rising from the depths to destroy the inhabitants of a dwarven city.
Perhaps they dug too deeply, or perhaps it was a summoning gone wrong, but whatever happened the result was death. A lot of it. Wherever this chthonic horror came from, it looks like a compelling big bad to me. I can see other exploratory groups sent in by the government to try and either capture the beast or recreate the conditions that called it into being in an attempt to acquire a new weapon to use against other worlds.
I did some reading during my vacation, but three books gave me ideas for the setting: The Long Earth, Anathem, and Marooned in Realtime. A combination of the concepts could give the answer for the unsolved mysteries of the setting.
Imagine parallel-ish worlds where some events in the past were different, but instead of just side-stepping into the other worlds instantaneously the journey would take an objective period of time while staying objectively instant. So, if reality B was relatively easy to reach and only took an objective day to reach you could step through the portal and arrive at that other reality. If you stepped back through the portal immediately and returned to reality A you would have experienced only a couple seconds of subjective time, but the time in reality A would have advanced by two days.
There could be a vast confederation of inter-dimensional empires. Anyways, I know this does not exactly follow my design concepts, but I was trying to figure out how a truly mysterious lost city would exist. I know that we have had lost cities before, at least from the Western/European perspective, but I am picturing a city on a scale larger than any lost settlements that have existed on earth. This would also allow the disaster that eliminated the previous residents of the megadungeon to have occurred relatively recently, giving an excuse for the environs to have not completely succumbed to nature.
