I don't know about a complete story, but I had a cool idea for the climax in K3.
The Exile and Revan board the Sith Flagship to fight the ultimate-power Sith Lord guy. After they defeat him (btw there's a huge space battle going on outside between the Republic and the Sith), Revan looks out the window on the Bridge and sees the Republic flagship that Bastilla was on get destroyed (Or, she could be using her battle meditation onboard, and a Sith strike team is sent to assassinate her, a la the same type of thing used against Revan pre-K1). During the whole game, Revan could be struggling with the lure of the dark side (Seeing Bastilla's ship destroyed, or feeling her assassination could trigger the anger that sends him over the edge). As the Exile is looking down at the Sith Lord's body, Revan is still looking out at the battle, and we see a sneer come across his face. All of a sudden, he spins around, his lightsaber (which could have been blue in K3) shines a bright red and he lunges at the Exile. You now take control over the Exile and fight against Revan to the death.
I just thought Revan betraying the Exile would be cool....Or the Exile could turn on Revan. You can choose which one, depending on which character you least like is that character that tried to betray you at the end.
Speaking of Betrayal, Did anybody notice that Darth "Traya" is part of the word "beTRAYAl"?
Kreia did sorta betray you at the end of K2, and I assume that was just a lazy idea from Obsidian to name her that.
Well that's my idea for a cool ending for K3
Visas and Bao-Dur should also do cool stuff in K3, since they were my favorites in K2
(Does anybody think that Kreia could have lied to you at the end of K2 when she was telling you the future?)