Although Grand Admiral Thrawn was defeated, his string of victories rallied the Imperial Remnant to stage a spectacular attack on the New Republic-held capital Coruscant. Whereas Thrawn wanted to capture the capital intact, these Imperials attacked without restraint and ravaged the once gleaming metropolis-covered planet. The Republic retreated and Skywalker commanded a number of missions into the Imperial-held world.

Stranded on Coruscant, 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 far away on the Deep Core world of Byss. There, in an ornate citadel, Skywalker faced an enemy he had not ever expected to see again: the reborn Emperor Palpatine.

Palpatine's spirit had been staving away death by using arcane Sith knowledge and cloning technology. Palpatine would grow clone duplicates of his own body to serve as tools for his evil life force should his body die. With this technique, Palpatine had escaped death several times. He called for Skywalker to kneel before him and become his apprentice. Skywalker, realizing that the Emperor was almost invincible, knelt before him, and agreed to join the Dark Side. Like a few others in recorded history, he believed he could defeat the Dark Side from within by learning its secrets. He had neglected one of Yoda's key teachings—never underestimate the power of the Dark Side. Skywalker, consumed by the darkness, found he was unable to break away from its snare. Though he succeeded in covertly sabotaging several of Palpatine's plans including a World Devastator attack on Mon Calamari, he could not bring himself back to the Light Side. However, with the help of his sister Leia, Skywalker was able to turn against his master, and together, they eventually defeated Palpatine finally.