Let just get off my chest. This is the second try by me to create a KOTOR 3 storyline.
You are a Jedi Knight who STAYED BEHIND and did not fight in the Mandalorian Wars. The Jedi Masters says so after all, and you know they are right. You sometimes wonder if that was the right desicion...
Anyway, 5 years past, the Jedi Civil War erupts and you fought in. Being one of the many Jedi Knights who stayed behind and remaining loyal to the Jedi Order, Atris tasked you on a mission to help defend a planet from an invasion by Sith Troopers. You are on a great ship, and everything seems fine. Then, the ship gets hijacked by Sith troopers who are trying to blow the whole ship up! [Tutorial Level as you play as the Jedi Knight and try to escape. You can exit this level if you wish.]
Sooner or later, you get out of the frying pan (the ship), and into the fire. The Sith captures you and takes you out while the ship explodes...
Planet 1: True Sith Homeworld
You wake up on their planet, inside of a Sith Academy, with all outside communications cut off.
You soon learn about these Sith. Wouldn't you know? They are not the Sith of Malak, but a new kind of the Sith, the True Sith (ring a bell?) These True Sith are Force-Using scholars, waging a secret war against the Jedi Order and the Republic.
The True Sith "persaudes" you to join up with their Order. You have the chance to say: "Sure!" or just lie, so that the Sith doesn't kill you. The True Sith then begin training you by putting you in excerises and puzzles. Think of this as Taris, only where the beggars are just as manlipuative bastards as you are. You also meet up with other Trainees...who happen to be captured Jedi Knights as well, conscripted into the True Sith army.
You learn next-to-nothing about this mysterious organization, other than that they are "true" and that they are "Sith". Sorry.
You meet up with 2 people, including your future Master, but their names are not important. The fact is, these 2 people hate the True Sith planet and decides to conspire with you a plan to escape this place. They would explain that they would send these people out on dangerous missions, and use them for their own evil activites, meaning that a Dark Sider Player would never want to conset to being used by the True Sith (they want to control the True Sith).
So, the 3 Characters start blowing up True Sith and finding a ship that could get them out of this mess. They do so succesfully, and then flee. They won't blow up the planet however, the player will return back to the True Sith Homeworld at the end of the game.
Planet 2: Coruscant
Years past, and the Jedi Knight has went into hiding, due to the threat of Nihilus that he instincally detected. After he learnt that a brand new Jedi Order is being formed, and he decides to waltz in and join.
This Jedi Order is basically based on the alignment of Exile. If Exile is LS, then the Jedi Order are Vrook/Atris-types, arrogant people who want to embrace the LS and force others to do the same thing. If the Exile is DS, then the Jedi Order is staffed with pretenders and Grey-Side Users, who secretly embraced the Dark Side and encourage others to do the same thing.
They review your application and then let you join in. You do random missions for them, and everyone is all fine and dandy. During one of your missions, you find T3-M4 nearby, serving the Jedi Order (and secretly helping out Revan). T3-M4 joins your party and will help you in finding the True Sith.
And then, your Jedi Council mention "disturbances in the Force", and realized that they are being caused by Sith Holocrons that are placed around the galaxy. One of your party members link these holocrons to the True Sith (note: Nobody in the Jedi Council other than you and your party members know that the True Sith exist, all they see is disturbances and send you on the mission without realizing the dangerous implications. If we are going to have a secret war, I think it would be better to have only a few people know about the threat, and to have NOBODY else ever find out).
The Four Planets In Search of the McGuffin/Sith Holocrons!
... you see a treasure trove of Sith Holocrons. These Holocrons are remeants of the True Sith that once taken over these planets. They also act as the "McGuffin". Wheter revealing about where Revan or the Exile is located, or stating exactly where the capital of the True Sith is...these Holocrons are key. Your mentor orders you to find these holcorons, and use this knowledge to find the True Sith.
(After you learn something from the holcoron, you could then decide to attack and destroy the Holocron for LS points, or keep the holocron alive to learn some secrets, gaining DS points and making you more powerful in the Force. You could also secretly be recurited by the Holocrons, who promise you infinite power if you ally with the True Sith... )
The Holocron each has a spirit of a dead Sith Lord, wheter if he is an an Ancient Sith Lord or a True Sith Lord. I really would like it if Kreia was one of the people in these Holocrons. If you blow the holocron up, the spirit dies alongside it.
Panet Five: The Endgame
You destroyed/saved the 4 mysterious Holocrons and you learn of the True Sith. You now get to fly back to True Sith Space to...
[This will be filled in later once I think of a suitable Endgame.]