Well, in one ending, you kill the Emperor and Vader and become the leader of the Empire if I'm not mistaken. So I don't think that one's canon.
You might be confusing that with the alternate ending to the Episode 3 game, in which you kill Obi-Wan, then the Emperor and take his place.
TFU's alternate ending basically has you killing Vader, then attempting to kill the Emperor, at which you fail miserably. You then become his mechanical slave. (Sound familiar?)