Looks like I only put the lightside ending. Whoops.
In the end, I wanted it to maybe create a base for a TOR-like game, except without that whole Revan plotline. Maybe just playing as members of the various factions. After that, since I think the "Galactic Sith War" (This war) would take a couple hundred years, if it were official it could set up novels and maybe a KOTOR 4.
When I had the Emperor say there was a greater threat, I had no idea where I was going with that. I've always wanted to explore the possibility of the Unknown Regions being the last home to one of the super powerful ancient groups in Star Wars, and the Sith being only slightly aware of them. Like how Malachor V was taboo to the Mandalorians, the home of whatever ancient race is taboo to the Sith.