Mystery dungeons... well, I can't say TOO much without spoiling future plot points, unfortunately, but I will say that there's a chaotic entity located in an unknown location that's controlling the spread of said mystery dungeons, and partially controlling the pokemon who live within them. Towns and cities are safe due to Arceus' protection. The fact that they constantly shift (though we're not going with the whole 'floor' thing due to how ridiculous it can be, Mystery dungeons do change every time another foreign pokemon enters) will make a LOT of sense once a certain team figures out who's behind all of it.

EDIT: you guys post like lightning, but Kabling will be a while, and I don't see too much wrong with your app. You can start if you'd like.