I think that Jolee was right in the game when he said that everyone thinks they're in greatest battle in history, when it actually just repeats itself. The same is with Revan & Malak in KotOR.
About the story in KotOR II, on the other hand, there's much to speculate about. If the game ended with DS, then maybe what the Rakatans told about the Star Forge was right. No one can handle it, not even Revan. It messed up his/her mind enough to kill Bastila and later destroying the Star Forge. After that he/she left to the Outer Rim to seek solitude from everything. During this, some powerful aspiring Sith Lords uses the Star Forge fleet in order to try to conquer the Core Worlds.
In the LS-ending on the other hand, the Jedi Order is in disarray due to the romance between Bastila/Carth and Revan. The remnant of the Sith uses this as their chance to kill Revan, but they end up killing Bastila/Carth instead. Due to the huge amount of feelings that's involved, Revan seeks solitude in the Outer Rim in order to calm down himself/herself and seek revenge when the time is right. During this period of time, some aspiring Sith Lords use the remnant of the Star Forge fleet (They weren't all at the Unknown World, were they?) to wage a new war against the against the unsuspecting Republic, which is going pretty successfully.