I think it was a long con by both the Emperor and Vader that blew up in their faces. They knew they had opposition so they decided to get those elements together and wipe them out, using Starkiller unwittingly as the instigator.
So:
Originally it seems like Vader and Starkiller are going to usurp the Emperor
EXCEPT Vader betrays Starkiller to the Emperor and kills him
EXCEPT Vader had only made it seem Starkiller was dead, so that he could now secretly go work on a new plan of gathering the seperate enemies of the Empire into one united fighting force (and I think this is where it is suggested Vader will take over as new boss of everyone)
EXCEPT Vader betrays Starkiller AGAIN and takes the Rebel leaders to the Death Star
EXCEPT Starkiller arrives on the Death Star, rescues the Rebel leaders, fights the Emperor, dies a martyr, encouraging the Rebel leaders to stay united and keep on fighting.
This all occurs in Star Wars: The Force Unleashed. It's a really good game and you should go play it.
