After his defeat in the False Emperor Flashpoint, his remains were somehow on a ship that crashed on Mustafar some 2,000 years after the end of the Cold War. Later, Count Dooku's Separatists reactivated him, and he went on a rampage, killing several CIS forces. His consciousness was uploaded in to the remains of the starship he was found in, but before futher action could be taken, Darth Vader stormed the base on Mustafar, marking the end of the Clone Wars. During the time of the Galactic Civil War, he contacted a group of spacers* via the comm systems of the ship where his "mind" was currently located, and asked them to locate and destroy a factory of droids based off of 47 himself. The band contacted accomplished the objective, giving HK-47 a new body in the process. He thanked them with a hologram of himself with "Meatbag" inscribed in it's base. He was eventually rebuilt into a jetpack, which was used by a spacer* during the same era.

*Spacer, in this text, refers to any given Star Wars Galaxies Player Character. This information is actually relevant to a quest series that came with the Trials of Obi-Wan expansion. As I never got to Mustafar, if someone can help me fill in what happened in between the last two sentences of this paragraph, please do so.

After being freed from stasis in the Republic Flashpoint Maelstrom Prison, he returned to the Foundry, but evidentally fell to the Dark Side again. After a battle with an Imperial strike team, he vanished in a burst of light. It is unknown whether he became one with the Force, or used the power Fold Space to flee the battle and escape to a distant planet.

When we last see Malgus, he has just been blown off a pit by a strike team. He managed to survive the battle that was the False Emperor Flashpoint, however, and escaped to an unknown planet.

All canonical player characters (Hero of Tython, Darth Nox, etc) do not have their ends mentioned in game or in any other online source. Personally, I presume they all either die of natural causes or fall in battle in the events succeeding the class storylines (though I like to think my pure Lightside Jedi Sentinel made a Holocron that Luke and his pupils later reviewed on Yavin IV, lol, so feel free to make up your own endings and your own "Legacies" for your characters).

Ah, Kephess. The final boss in Operation: Explosive Conflict and an abundant source of headaches whenever I go up against him. Apparently, in his battle with a powerful 8-16 man strike force, he was fatally wounded. He was saved by the Dread Masters, powerful Sith Lords who also were the "masters" who you hear so much of during the Operation (They once were one of Kephess's targets, but they enslaved him and used him as a weapon). He joins them in exile, vowing revenge on those who defeated him on Denova. A hint at future content, perhaps? Kephess 2.0? Having a migraine just thinking about it.