You beated it and never noticed Malak? Did u play it in your sleep? When u get to Korriban u first enter the Sith Academy and fight a bunch of Sith there. then on your way back from the Academy u enters a cave (which u passed by earlier, getting a message to visit it later). Then in the far end of the cave is a Tomb, where u revisit events earlier in your life. And u will also have to fight Malak, Bastilla, Kreia (and also the rest of your team if u want to) and Revan. All in vision, so u don't actually kill them.