In 4 ABY, Starkiller was sent to the incomplete Death Star II to await the Emperor, who was coming for an inspection tour. After Palpatine's arrival, Starkiller was sent to command the Imperial Fleet guarding the Death Star, keeping it on the far side of Endor. It was here that he sensed the arrival of Leia Organa along with the Rebel strike team coming to destroy the shield generator that protected the Death Star. When he informed the Emperor of this, Palpatine ordered him to oversee Imperial operations to prevent an attack on the Death Star's shield generator.

Starkiller ordered his long-term apprentice, the dark clone of Anakin Skywalker, to defeat the Rebels attacking the shield generator. In order to keep the clone's existence a secret from the Emperor, Starkiller also ordered his apprentice to kill any Imperial troops he encountered on the way. The clone carried out his master's orders and ensured the shield generator's safety, killing the smuggler Han Solo, the Wookiee Chewbacca, and Organa along the way.

Aboard the Death Star, Emperor Palpatine and Starkiller sensed the defeat of the Rebels on Endor. With the bunker secured and the shield generator still active, any chance that the Rebel fleet had of destroying the battle station with the two Sith Lords on it was gone. Just after Palpatine declared that the end of the Alliance marked a new golden age of peace for the Galactic Empire, he revealed his awareness of his apprentice's latest act of treachery. True to his nature, Palpatine gloated about how he knew about Starkiller's attempts to clone the original Skywalker since the beginning of the secret project on Kamino. In a desperate attempt to rid himself of his Master, Starkiller activated his lightsaber in order to strike down the Emperor. But Palpatine anticipated his apprentice's intention and countered with Force lightning, calling him "Marek" before doing so. Unable to bear the pain and the damage that the lightning caused to his armor's life support systems, Starkiller quickly fell to his knees in submission. The Emperor then commanded Captain Ignatius Sarkley to take his troops and kill the clone on Endor.

On Endor, the dark clone of Anakin Skywalker sat in meditation near Leia's dead body. As several Star Destroyers converged on his location, the clone opened his eyes and prepared to deal with the latest threat to himself and his Master's plans.