What if various Undertale characters absorbed the 6 human souls?
I can imagine Sans gaining more advanced fourth-wall awareness and messing with the game's code, but accidentally breaking the game because the code can't function properly when written in Comic Sans. The game ends up falling apart, and you end up fighting a couple of monsters made up of corrupted code. In the end, the game bricks and Chara deletes it, but not before Sans and Alphys round up a bunch of characters and retreat to your hard drive. If you were to reinstall Undertale, the characters would end up returning to the file, but now there are two of every major character (besides Flowey).
That could actually be a pretty cool AU. DuoTale, perhaps?