In the alternate ending, Starkiller kills Darth Vader, the Emporer offers him a place as his new apprentice, but Starkiller turns on the Emporer with his lightsaber. The Emporer was prepared, and then gravely injures Starkiller by Force-Pulling a ship through the throne room viewing port straight into Starkiller's body, which needs intensive repairs afterward, very similar to Darth Vader.
The Emporer basically tells Starkiller something along the lines... "You could have been my equal. But now you're just a tool, and like Lord Vader, when I find a new apprentice, you will be destroyed."