During the Imperial Era, specifically in the year 2 BBY, a confrontation unfolded aboard the Empirical, situated within the Dominus system. The Empirical, a significantly altered cruiser serving as the property of the Sith Lord Darth Vader, functioned as a mobile research vessel. It was utilized for conducting highly secretive experiments involving both prisoners and extraordinary alien species. The Empirical was crewed by Imperial officers manning the bridge, and its security detail consisted of a platoon of Imperial soldiers personally chosen by Vader.
Six months prior to this engagement, Darth Vader covertly moved the severely injured form of his unconscious apprentice, Starkiller, to the Empirical. Known only as "Subject 1138," the crew members believed Starkiller to be merely another subject of the Dark Lord's experiments. Consequently, the entire crew was caught off guard when Starkiller initiated an escape, breaking free from the medical bay. As the ship's military contingent struggled to subdue the apprentice, the holodroid PROXY steered the Empirical directly toward the Dominus system's star, acting on Vader's directive to safeguard the secrecy surrounding Starkiller's existence. Together with PROXY and the former Captain Juno Eclipse, Starkiller made his escape aboard the Rogue Shadow moments before the Empirical met its end in the star.
Following Starkiller's assassination of Shaak Ti, a fugitive Jedi Master concealing herself in exile on the planet of Felucia, he received orders from the Sith Lord Darth Vader to return to the Executor. Vader acknowledged Starkiller's success in eliminating one of the remaining members of the Jedi High Council, informing his secret apprentice that the time had come to overthrow Darth Sidious, publicly known as the Emperor Palpatine. Although Starkiller concealed his excitement from his master, he felt elated at the prospect of finally becoming a true Sith. The Emperor's downfall had been a goal he had trained for over the years, in addition to his service to Vader.
Before his return to the Executor, Captain Juno Eclipse inquired about her future role as the eighth pilot of Starkiller's experimental stealth starship, the Rogue Shadow. Due to Starkiller's growing connection with the female officer, he promised to support her military career. He also imagined his future as a Sith Lord while Vader replaced Sidious as ruler of the galaxy. Unbeknownst to Starkiller, Eclipse inadvertently learned of Vader's plot to assassinate the Emperor. Torn between her allegiance to her sovereign and her commanding officer, she reluctantly kept silent.
Upon his return to the Executor, Starkiller met with Darth Vader on the bridge of the incomplete Super Star Destroyer. They observed the Emperor's fleet of Imperial Star Destroyers converging on the Executor's location beyond the viewport. Starkiller initially believed that Vader had lured Palpatine into a trap, but he was proven wrong when Vader stabbed him through the abdomen with his lightsaber. Vader claimed that the Emperor's spies had followed the apprentice to the Executor. As Starkiller collapsed in shock and pain, Lord Sidious "entered" the chamber via the holodroid PROXY. Sidious angrily accused Vader of treason for training Starkiller in the first place, and ordered him to kill the wounded apprentice. Facing the threat of his own demise, Vader complied and used telekinesis to hurl his apprentice around the chamber. Afterward, he threw Starkiller through the viewport into the vacuum of space, much to Sidious' delight.
While Starkiller was unconscious, Darth Vader's droids retrieved his body from the vacuum and transported it to the Dark Lord's science vessel, the Empirical. The crew of the Empirical only knew Starkiller as "Subject 1138" and regarded him as another one of Vader's secret experiments. Starkiller remained in a coma for six months while his body underwent repairs. During this time, Starkiller believed he was dead and experienced numerous visions and memories. Upon awakening, he felt relieved at the end of the visions but became enraged upon seeing Darth Vader. While restrained on the operating table, Vader revealed that the "execution" had been staged. Vader explained that Starkiller's life had been spared to execute a new plan to destroy Sidious. When Starkiller considered defiance, Vader threatened to kill him by activating the Empirical's self-destruct sequence. However, Vader also pointed out that Starkiller had a second chance to fulfill his destiny as a true Sith Lord and seek revenge against Sidious. After a moment of consideration, Starkiller reluctantly agreed and was released from his restraints.
Darth Vader explained that with Palpatine's spies monitoring his every move, he needed a distraction to divert attention. As the laboratory droids provided him with a new lightsaber, Starkiller proposed an assassination, but Vader dismissed it, stating that no single act would gain Palpatine's attention. Instead, Vader tasked Starkiller with creating a rebellion to challenge the Emperor's rule over the galaxy; an alliance of rebels and dissidents. Vader gave Starkiller freedom in pursuing his objective. However, Starkiller was also ordered to sever all ties to his past, except for PROXY, to ensure his continued service to Vader remained a secret. Vader concluded his transmission with an assurance that the dark side of the Force was always with Starkiller, revealing that he had been communicating through PROXY.
PROXY was overjoyed by his master's survival, as it meant he could still have the opportunity to terminate Starkiller, completing his primary programming. However, due to Vader's orders, PROXY focused on ensuring Starkiller's escape from their current location. Through PROXY, Starkiller learned that he was aboard the Empirical in the Dominus system. PROXY then hacked into the ship's navigation system, setting it on a collision course with the Dominus star, as Vader wished for all witnesses to be eliminated. To ensure the demise of all Imperials aboard the Empirical, PROXY also jettisoned all of the escape pods.
When Starkiller inquired about Juno Eclipse, PROXY informed him that she was alive and aboard the Empirical. Her association with Starkiller had ruined her career, and she was declared a traitor to the Empire. As they encountered Imperial stormtroopers stationed aboard the doomed vessel, Starkiller activated his new lightsaber, realizing it was the former weapon of Jedi General Rahm Kota. Despite PROXY's reminder that Vader had ordered him to sever all connections to his past, the apprentice chose to head to the prison cell to retrieve Eclipse before the Empirical was destroyed.
As Eclipse regained consciousness, she was surprised to find Starkiller alive, despite being informed of his "death" aboard the Executor. Although Starkiller disobeyed Vader by saving Eclipse's life, he concealed the fact that he still served the Dark Lord. Declaring his allegiance to the Empire over, the apprentice brought Eclipse with him, explaining his actions by claiming he still needed her as a pilot. Explosive bolts severed the umbilical connecting the Rogue Shadow to the Empirical just as they boarded, and Starkiller ordered PROXY to fly the ship away from the science vessel as it collided with the Dominus star. Eclipse took control of the ship almost immediately, having regained most of her senses.
After their escape, Juno Eclipse confided in Starkiller her uncertainty about the future. Her former life with the Empire was over, leaving her unsure of what to do. Starkiller then revealed his plan to build an army to launch a full-scale rebellion against the Empire, intentionally omitting any mention of Darth Vader's involvement. With no other purpose to pursue, Eclipse agreed to aid his cause.
Before Starkiller could begin his rebellion, he realized he needed to establish contact with the Empire's enemies. He thought of Rahm Kota, the Jedi he suspected had survived their previous duel in the TIE Fighter Construction Facility above Nar Shaddaa. Their search for the general eventually led them to Cloud City on Bespin, where Starkiller was forced to defend Kota—drunk and depressed—from Imperial soldiers.
This particular conflict is absent as a playable level in the Playstation 2, PSP, and Nintendo Wii iterations of the game. However, the event is still depicted through cutscenes that showcase Vader's reconstruction of Starkiller, his revised mission objectives, and the rescue of Juno Eclipse from the ill-fated vessel.
Within the Xbox 360/PS3 version, Starkiller is designated as Subject 1138.