In the days following the Manehattan Incident, as it came to be termed, Aristotle and Spike began overseeing the cleanup of the area, due to a local law that said they had to. Karkat, meanwhile, inadvertently found himself addicted to anime in the course of finding out what those Mysterious Shouty Women were going on about. Apparently, they had been anime people. The world was getting too strange for him.
The Equestrian government revised its inter dimensional incursion protocols to be better prepared for the next such incident, though being a government initiative, this did not work out nearly as well as was hoped. Twilight Sparkle went into conniptions at Aristotle accidentally paradigm shifting all of Equestrian knowledge for the third time. The Hole in Reality's Wall was kept in the Bro Cave's basement, as there's not really much you can do with something like that. It later became the site of several other short-lived crossovers and eventually led to the Circle of Humans gaining a new addition in the form of a worn out sailor suit that could move on its own, but since it didn't do very much else, it was largely ignored. Poor guy.