A significant conflict transpired on Mustafar between the forces representing the New Republic and the X1 organization. X2, the former clone trooper who became a Jedi Knight, commanded the soldiers against his sibling, the Sith Lord known as X1, with the objective of destroying his laboratory filled with deranged clones. The New Republic forces were victorious over the Imperials on the planet, and X2 brought about his brother's demise.
X2, along with Grey Squadron, had successfully located X1 at Bast Castle located on Vjun and had breached the defenses of the fortress. X1 managed to escape to his cloning facility situated on Mustafar; however, by discovering a holocron, X2 gained the ability to track his brother's location. Consequently, X2 and Grey Squadron journeyed to the volcanic world with the intention of finding him and ensuring he faced justice.
The military of the New Republic launched an assault on the Remnant's Star Destroyer squadron while looking for Luke Skywalker, who had been taken prisoner. Subsequently, soldiers boarded the Star Destroyer, and after overcoming resistance, they destroyed the vessel and proceeded down to the planet's surface.
Following this, X2 landed on the planet, supported by Republic soldiers. They faced an attack from a group composed of stormtroopers and other combatants, including those belonging to Gizor Dellso's Rebellion, while simultaneously, X-wings and TIE fighters engaged in aerial combat above them. X1 was utilizing his cloning installation on the planet in an attempt to create a clone of Skywalker, and he deployed his clones of Wookiees to try and impede X2's progress.
X2 encountered X1, and they exchanged a brief dialogue. X1's appearance had now transformed to resemble Emperor Palpatine. X2 gained the advantage during their duel and had an opportunity to eliminate his brother. Nevertheless, he chose not to kill him, stating that the prisons located on Kessel would be sufficient to contain him. X1, employing a Force pull, attempted to pierce X2 with his lightsaber. X2 evaded the attack by jumping over it, resulting in X1 impaling himself before falling into the lava on the planet's surface.
X2, Luke Skywalker, along with the soldiers of the New Republic, went back to their frigate, making preparations for all the difficulties that came with the New Jedi Order and any other challenges that might lie ahead.
The Nintendo DS version of these events unfolded somewhat differently. In the DS version, it is suggested that X1 reactivated the Separatist Droid facility on Mustafar to gain additional manpower, and X2 had to unlock the facility's entrance by activating several switches. Furthermore, the reference to cloning Luke Skywalker was omitted, implying that X1's motivation for kidnapping Luke Skywalker was simply driven by spite. Additionally, Luke encourages X2 to engage X1 in a solo battle as a means of testing his strength in the Force. Also, X1 and X2 immediately fight with no help from anyone, meaning that the clone Wookiees and Stormtroopers who aided X1 in trying to defeat X2 were not in the DS version. Finally, the final dialogue between X2 and X1 was made longer, especially on X1's part.