It was at this time that rumors surfaced of a Jedi Master hidden on the remote world of Wayland. Luke investigated, finding the insane Dark Jedi clone, Joruus C'baoth. Luke's compassion defeated his safety instincts, as he studied with C'baoth, and tried to draw him from the madness and grip of the dark side. C'baoth's insanity and evil was too deeply rooted to undo, and in his bid to mold Skywalker into his new dark side pupil, C'baoth did the unthinkable. Using Luke's severed hand recovered from Bespin by Imperial agents, C'baoth grew a clone of the young Jedi -- Luke Skywalker -- and sent the mindless duplicate to kill Luke. Skywalker eventually defeated C'baoth and the clone.
During this crisis, which played out while the Republic was besieged by the depredations of Grand Admiral Thrawn, Skywalker also met Mara Jade. A fiercely determined and highly skilled Force-sensitive warrior, Mara was once a trusted agent of Palpatine. She was one of Palpatine's "Hands," an elite assassin and agent who could hear the Emperor's call from across the galaxy. Jade held Skywalker responsible for the ruination of her career and purpose, and longed to kill him. Despite repeated opportunities, Jade did not kill Luke, and the two worked together to undo Thrawn and C'baoth's plans. Blunting her hatred for him, Mara developed a begrudging respect for the Jedi and his skills.
Although Thrawn was defeated, his string of victories rallied the remaining Imperial warlords to stage a daring and violent stab at the Republic-held capital of 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, Luke 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 Luke, and deposited him far away on the Deep Core world of Byss. There, in an ornate citadel, Luke faced an enemy he had not ever expected to see again: Emperor Palpatine.
Palpatine had long been staving death away by using arcane Sith knowledge and cloning technology. Palpatine would grow clone duplicates of his bodies to act as receptacles for his evil life force should his body die. With this technique, Palpatine had escaped death time and again. 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, Luke 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 himself unable to break away from its pall. Though he succeeded in covertly sabotaging a number of Palpatine's plans, he could not bring himself back to the light. With the help of his sister, however, Skywalker was able to turn against his master. Together, the Jedi twins were eventually able to defeat Palpatine once and for all.