Lets assume he lives, and flees into the Unknown Regions as Wookiepedia pretends his does, what does he find their, what has he already found their? During the Cold War Malgus concerned himself with expanding the Empire's territories in the Outer Rim, perhaps he found ancient Rakata Technology (Rakata seems a defining feature of the Old Republic Era) or some other form of weapon. He already had control over the foundry so that could have lead to some clues. So perhaps Malgus returns with this new power, and is reaccepted into the Empire (who by know will have accepted his is right) and this knew power is used against the Republic, with Malgus and Marr at the helm, and the Emperor scheming in the shadows.
Malgus himself is unlikely to play any future roles, considering Lead Writer Hall Hood has confirmed that Malgus is dead. If anything, his only known apprentice, Darth Karrid, would continue his path. Then again, the Sith Inquisitor may also do something to similiar extend since he/she also supports the change within the Empire, to what extend that happens is of course up to the player.
As far as "plot devices" go, there is still the Infinite Engine from Revan's complex on Nar Shaddaa. Let's say a powerful Sith Lord (like that ominous Keeper of Mysterious or Darth Nox, who afterall is in charge of the Pyramid of Ancient Knowledge) gets a hold of it and manages to make it grow very fast through some sort of Dark Side ritual, they would have the means to get themselves another Foundry or Star Forge.