A battle occurred on Mustafar between the forces of the New Republic and the X1 faction. The clone trooper-turned Jedi Knight X2 led soldiers against his brother, the Sith Lord X1 to destroy his laboratory of insane clones. The New Republic troops defeated the Imperials on the planet, and X2 killed his brother.
X2 and Grey Squadron had tracked X1 to Bast Castle on Vjun and had infiltrated the fortress. X1 escaped to his cloning laboratory on Mustafar, but by finding a holocron, X2 was able to track his brother. X2 and Grey Squadron traveled to the fiery world in order to find him and bring him to justice.
X1 and X2 duel in a Star destroyer over the planet.
The New Republic forces attacked the Remnant's Star Destroyer fleet in search of the captured Luke Skywalker. Soldiers then boarded the Star Destroyer and after fighting off resistance, destroyed it and preceded to the planet surface.
X2 then landed on the planet with the support of Republic soldiers. They were attacked by a group of stormtroopers and other forces, including those of Gizor Dellso's Rebellion, while above them X-wings and TIE fighters were still fighting. X1 was using his clone facility on the planet to try and make a clone of Skywalker, and released his clones of Wookiees to try and hold off X2.
X2 saw X1, and they exchanged a few words. X1 now looked similar to the Emperor, Palpatine. X2 got the upper hand in the duel and had a chance to kill his brother. However, he refused to kill him, saying the prisons on Kessel will hold the pieces. X1, using a Force pull, tried to impale X2 with his lightsaber. X2 jumped over the blow and X1 impaled himself, before falling into the lava of the planet's surface.
The defeated X1
X2, Luke Skywalker, and the New Republic troops returned to their frigate, preparing for all the challenges of the New Jedi Order and whatever else lay ahead.
The DS version of the events played out a bit differently. In the DS version, it is implied that X1 reactivated the Separatist Droid facility on Mustafar for additional manpower, and that X2 had to open the door to the facility by activating a few switches. Also, the reference to cloning Luke Skywalker was cut, and as a result, the reason for X1 kidnapping Luke Skywalker was implied to just be out of pure spite. Also, Luke encourages X2 to fight X1 by himself as a test to his strength in the Force. Also, X1 and X2 immediately battle with absolutely no aid from either side, meaning that the clone Wookiees and Stormtroopers aiding X1 in trying to defeat X2 was not in the DS version. Lastly, the final words between X2 and X1 were lengthened somewhat, namely on X1's part.