I couldn't spot this elsewhere, please correct me if it is.
I'm assuming here that some have played the PMD games, and will know the main concept is forests, with floors stacked one above the other with stairs. The games give little explanation for their existence. PMD itself goes for the inferrence of 'A wizard did it', whereas PMD2 tells you 'because Mystery Dungeons' (thanks NP).
So, I'm stumped. Anyone else have an concept as to why, or how, these structures exist? Have they always existed, or do they exist solely as the plot calls? And WHY does a Pokemon feel the need to join you after you punch it to fainting?