Starkiller was kept secret by the Emperor so that Vader could eventually use Starkiller to overthrow the Emperor, however, the Emperor discovered Starkiller and Vader was forced to kill him. Despite the apparent demise of Starkiller, Vader decided that he did not want to part with his powerful apprentice and salvaged his body to be resurrected. Starkiller was commanded by Vader to forge an army against the Emperor to distract his attention whilst Vader conjured a new plan to overthrow the Emperor.
Starkiller was given a pilot, Juno Eclipse (who he kindled a romance with), and had the help of his long-time companion, PROXY, and a rogue Jedi, General Rahm Kota (who Starkiller actually dueled and blinded as a Sith). As Starkiller's list of allies grew, Vader decided that he didn't want to overthrow the Emperor after all so Starkiller returned to kill him. Attacking the Death Star, Starkiller attacked Vader and severely damaged his armour.
Laughing, the Emperor offered Starkiller a place at his side as a Sith Lord, but only if he killed Vader. Starkiller rejected the Dark Side, instead attacking the Emperor. Knowing he could not best the Emperor, Starkiller held him off to allow his friends to escape and was killed.
Despite his death, Starkiller inspired the creation of the Rebel Alliance which would go on to destroy the Empire and kill the Emperor in his name. Vader went on to make several clones of Starkiller to use against the Rebellion, however, all but one turned good and killed the 'true clone' (i.e. the failed evil one) and one clone, the 'pure clone', ended up finally getting with newly-promoted Rebel Commander, Juno Eclipse.