In the beginning, Malgus and his Master Vindican had led the victorious recapture of the Sith world Korriban, before the former struck down the latter for being injured at the hands of Jedi Master Kao Cen Darach. At the height of the war, Malgus led a surprise assault on the Core World of Alderaan; though initially successful, Malgus and his forces were defeated in a concentrated Republic counterattack led by his nemesis from Korriban, future Grand Master Satele Shan. The Sith Lord was heavily wounded during the battle, and was forced to wear a respirator for the remainder of his life. In 3653 BBY, the Empire entered into sham peace negotiations with the Republic, which were truthfully nothing more than a distraction from the Sith's true target: the Republic capital of Coruscant. Malgus was chosen by his superior Darth Angral to participate in the attack on Coruscant as the leader of a strike team that would invade the Jedi Temple. Malgus succeeded in killing a substantial number of Jedi defenders — including Jedi Master Ven Zallow, who has been recognized as Malgus's most notable kill — before the Sith fleet arrived to lay waste to the rest of the world. By the end of the engagement, the Sith had destroyed the Jedi Temple, killed half of the members of the Jedi High Council, and disgraced the Jedi Order in the eyes of the Republic.
Although Malgus had been under the impression that the Imperial Armada was going to raze Coruscant and destroy the Republic once and for all, the battle was ultimately used only as leverage in the peace negotiations on Alderaan. While the Alderaanian summit progressed, the Sith settled into an occupation of Coruscant. Malgus was placed in charge of orbital security, but the Sith Lord defied his orders and traveled back to Coruscant's surface to strike against the renegade Jedi Aryn Leneer, who was targeting Malgus for his murder of her Master, Ven Zallow. Although Leneer ultimately failed, the conflict caused Malgus to become disillusioned with the Empire and to review his relationship with Daru as a weakness. Thus, he was forced to kill his lover to preserve his own power, which he later used to cleanse the Empire of the politicians whom he blamed for allowing the Republic to survive. During the Cold War years that followed the successful peace negotiations, Malgus led Sith forces into the Unknown Regions, claiming previously-unknown territories for the Empire.
After his death at the hands of a Sith task force one of his followers Dark Council member Darth Xedrix found themselves on the remote world of Earth. Landing in ancient Egypt they were worshiped as the gods when Xedrix telekinetically choked a servant, he was seen as Anubis the God of death, Xedrix carried the holocron carrying the spirit of Malgus so that he may one day return. Under a false pretext the Egyptians had already begun construction on the pyramids bug Xedrix ordered them to resemble a Sith holocron.
Malgus's holocron was locked away in the great pyramid of Giza for three thousand years until being discovered in 16BBY by Shawn Mendes. Upon being released Malgus's spirit fled to Mars looking for the Sith outpost used during the Sacking Of Coruscant but instead found the planet deserted and barren, then he rembered who'd released him from Chaos and sought him out. Malgus was impressed by Shawn's natural ability with the Force and began communicating with him offering advice which Shawn turned his nose up at.
For a short time he was able to take control of Shawn's body but that spent most of his power, only making himself or heard by Shawn Malgus esstienly followed him everywhere. When he wasnt Malgus traveled the Galaxy collecting information of what has happened in the three miillenia he'd been gone,