And what if you're darkside? your mission would be to kill them? hmm, sounds like the dark path might not be available until late in the game, since no jedi is going to unite under the sith banner. You might turn fully light or dark when you choose a prestige class, kinda like your 'choice' at the temple.
My guess is that you could recruit other Jedi for a just cause at the onset. Then when your decisions begin to put you on the dark path some of the other Jedi will be corrupted alongside you. If party members can change alignment now, I wouldn't be surprised if a Jedi NPC can eventually become a Sith.
After that the main goal might be to supplant the current Sith rulers and take their positions of power for your own. That is kind of like the original KotOR though. So maybe not.