If you picked Light Side:
After speaking with the last Jedi, Kreia telepathically summons you to her quarters - 'It is time I told you everything, exile'.
On the way down the Ebon Hawk corridor you are stopped by the Handmaiden/Male guy (forgot his name, will edit when I know). She tells you to be careful, Kreia has been acting more strangely than usual. You can either thank them and take their advice into consideration, tell them you think they are wrong, or rudely reject them. You then walk into Kreia's quarters. She tells you that you must travel to Dantooine so you can get the truth from the Jedi Masters. She also comes clean about her involvement with Revan, tells you what Revan told her before he left for the Unknown Regions (depending on whether he is light/dark).
The Hawk lands on Dantooine. Depending on whether you helped the Mercs or not, the leader of Khoonda greets you and tells you Master Vrook has gone off to the Academy Ruins. While talking to the Khoonda leader, Bao-dur and Atton run in, telling you that you can't go into the Academy alone.
Your party heads to the Academy only to find the complex completely rebuilt, and the front door open. You enter, and see the insides also refurnished, with the fountain once more gushing clean water, and vines hanging down from the ceiling. You enter the main chamber to find the Jedi Masters, who explain to you that you are a wound in the force, etc etc (basically all of the dialogue from the game). They then try to rob you of the Force, Kreia enters and slaughters them, and stuns you.
You wake up and get some new force powers (Dark Side: Force Crush, Force Minion (you destroy your enemy's mind and use him against your enemies), Force Hover (your character is temporarily given the ability to fly by using the Force - this will come into play later) Light Side: Force Enlightenment, Saber Mastery (now you fight like a REAL Jedi). Your FP also increase and you automatically gain a level (your exp you gained before stays the same). As you go to leave the Academy, Bastila enters.
Depending on whether Revan turned light/dark, Bastila either tells you how Revan brought her back from darkness, or joined her in it. She then explains what happened when Revan left and tells you, after much consideration, she wants to join you to go and find him. But first you must both travel to Telos to stop the Sith.
As you leave the Academy you find Bao-dur and Atton on the floor, almost dead. If you are light side you take them back to the Hawk. If you a Dark, you can finish what Kreia started and suck the Force from them. If you chose to save them, then back on the Hawk once they recover, they realise they are Force Sensitive.
The rest of the story runs by KOTOR2's interpretation until you arrive on Malachor V. The Hawk crashes as usual, however this time you see a cutscene of all of the passengers getting out, and then seperated by a rockslide. You are left with Bastila and Atton (Bastila has by now filled the empty party slot that was formerly Kreia's).
You head through the canyons that make up Malachor V's surface, having to kill the force beasts that you encounter. However you also see the twisted corpses of Jedi and Mandalorians on your travels, and cutscenes play of the final battle of the Mandalorian War as you remember what happened that day. Kreia sends you a message through your bond, taunting you, spurring you on, as you reach the large clearing where the extra large beast attacks you.
You now change to Bao-dur, the Handmaiden/Male guy, and Visas. They managed to survive the crash and subsequent rock slide and are now doing their best to reach you. However they are on a different map to you, and must find an alternative route to Trayus Academy. There is no sign as to whether the three droids survived the crash. Mandalore is lying unconscious on the opposite cliff side.
You now change back to the Exile, Bastila and Atton. You go on to reach the Academy and make your way through the first section, choosing either side to go into next. Bao'dur's party reach the Academy moments after you enter, only to be stopped by Darth Nihilus - 'Did you really think you could defeat me so easily? As long as the Force exists, I can never truly die. You know this to be true'. He encompasses the party in a stasis field, and casually cuts down Visas. The other two struggle to resist as Nihilus turns to them.
You now change to Mira/the wookiee, who have found Mandalore and given him treatment. They watch as Nihilus kills Visas. Mira would say 'No' or something to that effect, Mandalore would watch silently, and the wookiee would give a bellow of pleasure at seeing the spectacle. The wookiee would then appear to try to kill Mira, but Mandalore kills him. 'I've come to the end of my road, Mira. I never wanted this to happen...not to my companions, the group I have grown to honour and treasure'. Mandalore runs off into the wilderness. Mira goes down to the Academy.
Meanwhile the Handmaiden and Bao'dur are fighting for their lives against Nihilus, having broken free of his stasis field. Mira arrives, and the fight truly begins - the fight which you are in control. If you defeat him, you see a cutscene of him being driven into a chasm. Bao'dur then goes off with his remote to activate the computers on the downed ships for the Mass Shadow Generator. If you are beaten, you watch the party being slaughtered.
The rest goes forward like KOTOR2 did, Sion dying, etc, until you reach Kreia at Trayus Core. She seems genuinely surprised that Bastila came, 'I did not expect you to come, Jedi Shan. After your experiences with Revan I would have thought you to have left the Force behind, as did so many others'.
'I am a true Jedi, Kreia', Bastila replies, 'And the Force is my ally, as it ever shall be. You detest it - you can never use it to do good. And that is why you must be finished here'.
You go into a fight with Kreia. Once you defeat her the first time, no stupid lightsabers appear. Instead, Kreia uses the Force to push your party members back as she leaps onto a ledge to recover. Lightning strikes the red part of the platform, and you see Nihilus slowly but surely climb over the edge, onto the platform, and make his way over to you, restored.
'I took great pleasure in cutting the blinded Jedi down', he mocks. 'It is now your turn.'
'NO!' Kreia screams. 'The Exile is MINE to deal with! I have made sure of it! I will not let you ruin everything I have worked for, Kun!'
Yes....Nihilus bursts into cruel laughter, reaches up and removes his mask...to reveal complete blackness behind. His shape is formless.
'Now you understand...why the Force obeys my every whim....why I feed upon it....I AM the Force.'
He tosses away his red lightsaber and instead fires out force lightning, frying Atton on the spot and knocking you back. Kreia howls again and dives down, catching Kun unawares and they both tumble over the edge into the core.
'Send the signal now, <Your name>' Bastila shouts. You press a button on a commlink, and Bao'dur picks it up, ordering his remote to blow the generator. Then you see the Hawk flying over to the Iridonian and his droid, picking them both off, before racing off to you and Bastila at the Core.
You just about make it out into Space before the planet blows. You now see a cutscene of the tattered remnants of your crew - HK-47 (if you repaired him) and T3 survived, they are the ones who piloted the Hawk to your rescue. G0-T0 has gone missing, so has Mandalore. The others, depending on whether they had survived or not, look tired and beaten up. Mira is tending to your own injuries. Bastila is with you.
'We must find Revan.....something tells me he will know how to heal the rupture in the Force that you inadvertantly created.....and he holds the key to the galaxy's future'. You then ask what happened to Nihilus and Kreia.
'Kreia is no more, of that I am certain. Nihilus is a spirit of his former self. He was eradicated at Malachor V when the Ravager was nearly destroyed, at the end oft he Mandalorian Wars. Like the spirit of Exar Kun, he cannot be destroyed...;
You then ask what happens next. 'I am afraid I cannot see what will happen...this is just one of the many mysteries of the Force, something you must find out for yourself. But do not worry....you will find all of the answers soon'.
The Hawk flies off towards a mysterious nebula in the Outer Rim....and the credits play.
If you chose Dark Side, it is as the above, however at the end, after Kreia falls over the edge with Kun, you can choose whether to slaughter your comrades or bend them to your will. And the final cutscene shows you, alone, in the ****pit of the Ebon Hawk, yellow eyes glowing, and a strange voice echoing....'Exile, I will have my revenge'....