So... the fleshing out of Connected Cosmos: The Game is taking longer than I thought it would, but I have figured out what the eldritch monster main villain is and how it's affecting the code-napped Crossover Update universes.
I call it The Twilight. It's a pocket dimension made entirely of...for now let's call it highly corruptive mostly sentient anti-magic with a psychic hivemind structure. That's a massive oversimplification but I don't have the energy to explain the whole thing. It's invading the universes that make up the game's main areas by leaking through cracks in space-time, which creates shadow monster drones, possesses and transforms powerful and/or weak-minded beings, and slowly terraforms the universe surrounding the cracks.
Rising Star Circus actually got off...sort of lucky. While their full universe got thoroughly borked, the circus itself became part of the main hub universe, a gilded city of Sorcery on a mountaintop called Mount Nexus, which just so happens to be one of the few universes that the Twilight can't enter...outside of certain story events, of course.
Then there's Harmonia (scaled down somewhat so it's not bigger than every other map combined, so as to save on resources and not be suspicious), where Lumiere has somehow managed to cut a deal with the Twilight. At least, he thinks he has. All ten kingdoms are dealing with some sort of thematically appropriate catastrophe thanks to some powerful boss-type character being fed by a massive Twilit Rift (what I'm calling the cracks the Twilight are using) in each of them. Luminos got it worst off, with Lumiere setting up shop there and Queen Melody and most of her staff being possessed (Nimbus and a few others managed to get away).
Dreaming Gaia is... sort of okay? On one hand the Twilight aren't that much more threatening than the stuff that's already there outside of being an outside-context problem, on the other hand they resonate with Nightmare energy and the remnants of both cults are interested in them for different reasons.
And then Renata has no way to fend off extradimensional shadow monsters so they're kind of in the midst of an apocalypse right now. So on top of her occasional bouts of frantic lucidity due to her half-dose of the memory suppression virus she's also having to survive the potential end of the world with no idea if the few loved ones she can consistently remember are alive or dead. On the plus side the Twilight are close enough to Heartless that her Keyblade finally ends up manifesting to protect her.
Also, the Twilight are programmed with the secondary function of keeping anything from entering or exiting the game without the proper permissions. By force.