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Return of the Emperor

Stranded on Coruscant in 10 ABY, Skywalker began to discover strange clues in newly opened secret chambers throughout the former Imperial Palace, clues to the Emperor's power. Before he could piece together their significance, a raging Force Storm appeared in the sky. The swirling vortex of dimension-altering energy consumed Skywalker, and deposited him in a cell aboard an Imperial Dungeon Ship bound for the Deep Core world of Byss. There, in an ornate citadel, Skywalker faced an enemy he had not ever expected to see again: Emperor Palpatine.

Darth Sidious spirit had been staving away death by using arcane Sith knowledge and Spaarti cloning technology. He would grow clone duplicates of his own body to serve as tools for his evil life force should his body die. With this technique, he had escaped death aboard the second Death Star and now called for Skywalker to kneel before him and become his servant. Skywalker, realizing that the Emperor was all-powerful, knelt before him and pledged to learn the ways of the Sith from him.

Luke, turning to the Dark Side.

Luke, like only a few other individuals, believed that he could defeat the dark side from the inside. However, he had underestimated the power of the dark side, ignoring one of Yoda's most important lessons. Skywalker worked for the light side in the shadows just like Quinlan Vos had during the Clone Wars. And just like that Jedi Master, he found he was unable to break away from its snare once he was immersed too deeply in it. During this dark apprenticeship, Luke acquired two Imperial Sentinels, clones mutated into his dark-side servants. Though he succeeded in covertly sabotaging several of Palpatine's plans including a World Devastator attack on Mon Calamari, he was too deep in darkness to think clearly.

When Leia arrived on Byss to rescue him, she succeeded only in getting herself captured, along with Han. However, Leia's light-side presence allowed Luke to partially shake off the dark side, giving him the initiative to rebel against Sidious fully. He aided the escape of her and Han and supplied them with the interface codes that controlled the World Devastators on Mon Calamari. He then turned to the Emperor.

In a failed assassination attempt, he marched into the cloning lab and smashed all the cloning tanks just after Sidious's current body expired. However, before he could finish the job, Sidious managed to transfer into one of the last living clones. When Luke attempted to subdue Sidious, citing that his time as a Sith apprentice had taught him the Emperor's weaknesses, Sidious scoffed at him and seized one of the lightsabers he kept in the lab. The two engaged in a quick lightsaber duel, but Luke fell before Sidious's brutal blade work. The Dark Lord then traveled to Pinnacle Base in his flagship, Eclipse, bringing a broken Luke along. However, with the help of his sister, Leia, Luke was able to fight back the darkness before it consumed him and turned against his master. Skywalker finally defeated Sidious in single combat. This confrontation was foretold by a Jedi Master a thousand years earlier.

Unfortunately, Sidious summoned a massive Force storm and began to systematically destroy the New Republic fleet around Pinnacle Base. Luke, together with Leia, created a massive wave of light-side energy that cut off Sidious's control of the storm, turning it against him. While they fled, Eclipse was destroyed, and Sidious's current incarnation along with it.