This is what I've got so far in my personal canon.
It's two years after The Sith Lords. A civil war breaks out between the Sith, caused by destabilisation of their leadership as a result of assassinations of key leaders. This gives what remains of the Jedi, the Republic and the Mandalorians a chance to defeat the Sith. The new main character was a Padawan from the Jedi Civil War who "switched off the lightsaber" and is now being hunted by the Sith...
Revan and the Exile were the ones responsible for the assassinations. The emperor, Lord Astaroth, doesn't know that and thinks the Sith Lord Darth Ra, was responsible. Ra took the credit for it to get closer to Astaroth. She showed him proof that the dark council were planning to overthrow him.
Little does Astaroth know, though, that Ra wants to become the new emperor herself. She had a vision of a Jedi Knight defeating the emperor. She tells Astaroth about her vision and requests to hunt down the Jedi Knight, as there is possibly a link between them. Astaroth agrees to this and sends a group of assassins.
Ra kills the assassins and finds the player, warning the player about the Sith threat. Ra shows the player the bodies as proof and offers to train the player in the ways of the force again. Ra, like Kreia, is hiding her real identity. She says that the Sith may be hunting you because they believe you to be of importance, but she pretends not to know what that importance is.
The player accepts Ra's offer for training. Astaroth senses Ra's betrayal and so throughout the game assassins are hunting Ra and the player. Ra won't take you straight to the unknown regions because a) you're not ready to face Astaroth; and b) it would blow her cover.
Last edited by The Lord of Chaos; 01-05-2013 at 01:39 AM.