The greater enemy that Revan foresaw was the Sith Emperor.
Much of the initial focus in SW:TOR (which can be considered in a way to be KoToR 3) is given to the sudden re-emergence of the Sith Empire, and their blitzkrieg attack on Republic planets. An easy interpretation of Revan's warning was that this mighty empire was hiding in the shadows and ready to attack at any time. This tends to fall apart given that Revan himself used the name of Sith, as well as the Dark Side, in his misguided attempt to prepare the Republic. The Sith Empire, for all it's evils, was an acceptable outcome and not what Revan was worried about.
The Sith Emperor on the other hand (known also as Valkorion, or as Lord Vitiate), is a shadowy figure even to his own people. His goal is true immortality, and he's already made some headway on it. He captured Revan and what remained of Revan's followers shortly after Revan came back to the Outer Rim hunting for him, and has kept both himself and Revan alive in the intervening centuries (Revan has gone quite a bit mad as a result). The Emperor puts the Sith Lords seen in KoToR 2 to shame in sheer power. He set up the war - which the Sith wanted at any rate - specifically to draw strength from the deaths it would provide. He would sacrifice anything and anyone - people, planets, up to and including his entire Empire - if it aids his quest to become immortal, and thus stands as the true foe for the series as a whole, even for those allied with the Sith.