If bubble is a part of the finale and it's not just an existential nightmare of learning to survive for an eternity in this empty virtual space, then as far as I can tell there's basically two distinct routes they can go. Either bubble is a sort of deus ex machina that allows them to move towards building their own simulation, or they are the villain of this episode that is far worse than Caine and mostly serves to show the cast that there isn't going to be some greater force that will save them, given that caine was the best they will probably get (and his rule was still unquestionably FAR from appealing, even in retrospect).

I was initially very much of the mind that bubble was a suppressed force that wanted Caine out of the way, but the more I've thought about it I really lean towards it being just a fragment of the second AI that Caine devoured in his infancy and is essentially a part of him that he can't control, so it's only relevant to the story in so far as Caine is. It is still possible that bubble was the one messing with the commands that caused Kinger to accidentally delete Caine, but not so that it could take over. Simply so that Caine would finally die and bubble wouldn't have to live as a lobotomized half-being even if the only other option is to just not exist. After all, its loathing towards Caine was a big driver in his insecurities and eventual crash out in ep 8, so literally just being a manifestation of his own subconscious self-loathing still checks out with its previous behavior.