Maybe it could be like the Genoharadon in KOTOR or that Kuja guy from Final Fantasy IX where the main Sith reveals himself AFTER you killed the last Sith Lord. Of course, if they really wanted a Kuja angle, they'd have to make him a narcissistic girly man dressed in drag with a tail.......wait a minute.....that's Atton Rand!
That would be hilarious: You just killed the last Sith Lord, when Atton Rand levitates down, dressed up in a drag costume all pretty and feminine, and says "I truly love you all" and goes on how you now took out everything that stands in his way of making the galaxy his fruity kingdom, and offers you to join him or become a part of his palace's foundation. Then, if you say no, and Revan took the Darkside route in KOTOR1, Atton flies off to the Star Forge, and you must pilot the Ebon Hawk into a giant purple orb glowing above it and.............ok this is just getting goofy.