It starts off on a space station in the unkown regions under the rule of the true sith. The true sith are ruled over by the remnants of the species sith (which were a race incredible strong in the force that had long since died out, or so we thought) and the decendants of the jedi who were expelled from the Republic after the order first split over a millenium ago.
Revan (who will be the eventual PC player), after waging a personal 4 year war against the true sith has been finally captured. However his apprentice Pheonix who we will play as for the meantime, was able to escape and under Revans order returns to the Republic with vital info regarding size, strength and strategies of the new threat. He finds Bastilla and the new Jedi order, containing members from kotor1 and 2, who against Revans direct orders plan a rescue mission.
With Phoenix's info, a strike team that includes members from 1 and 2 (not just jedi) goes in search of Revan. However Revan has been transfered a secret facility, and the party must now search throughout the Sith empire for clues portaining to where Revan is. After visiting a couple of planets we find him, however in the meantime the Sith have finally launched their assault on the Republic.
Revan now takes the lead and with the help of his party they must track down the Sith homeworld whence came the species Sith and the original Sith teachings and which is now the base for their attack. how you have been playing the game light or dark will climax here where you can destroy the threat or assume the dark throne. Most of the game will largely take place in the unkown regions which will give it a new fresh feel.