Seeing as KOTOR 2 is still my favorite all-time game, let me try and come up with a plot for a possible sequel whilst accommodating TOR. I haven't actually played TOR but I have seen what happens with Revan and the Exile and thought it was terribly done but I still intend to theorize around it.
So as all KOTOR games begin, your created character wakes up not knowing what exactly is going on. The player's homeworld is under attack and after picking up your standard gear joins the fight against the mystery invaders. During this, a mysterious voice aids the player and you eventually escape on a Republic escape vessel which takes you to Coruscant. Once you arrive on Coruscant, you enter into a massive 'pen' of sorts, like the Refugee Sector in KOTOR 2 but much bigger and you are a refugee. The overseeing Republic forces explain that a devastating bio-weapon has been used in the attack on your homeworld and on many other planets and that all survivors are in quarantine.
However, you eventually catch word of a group of refugees who plan to slip past the quarantine and escape. You meet with them and do some quests to earn their trust, like drugging some sentries and you have the option of using lethal or non-lethal drugs depending on your light/dark allegiance. However the night before the escape, the voice makes a return and you find out it belongs to the Exile who as we know from TOR can Force Ghost. She explains that the plotters of the escape are in fact Sith spies looking for a way into the heavily guarded Republic capital, except for one member of the group who is in fact an undercover Jedi, seeking to uncover Sith intelligence networks.
Here, the paths deviate slightly.
For a light-sided player, you reveal to the Jedi that you know their secret but agree to help him/her. The escape goes off without a hitch until they make it out of the quarantine area, where thanks to the Jedi, their are soldiers waiting for them. The spies are arrested and the Jedi (who vouches for you) are free to go. He/she explains that they agreed to your help as you are force-sensitive (surprise, surprise) and that whilst you would normally be too old for training, an exception must be made when every soldier is needed.
For a dark sider, you reveal to the spies that their is a Jedi amongst them and after a fight the jedi is killed. You all escape but when you go to leave them, they knock you out and take you prisoner. You then wake up in a safehouse and are introduced to the force-sensitive head of Sith intelligence on Coruscant who reveals you can feel the force. He/she offers you training and a place with the Sith, both the Jedi and the head of SIth intelligence serve as the player's mentor and party member.
The general plot here, is that both sides are in a race to find a series of keys, to a vault hidden under the Jedi Temple. In this vault, is a powerful force nexus (or something like that) which can be used to draw on the power of dead force users. It being so powerful, the Jedi built their temple on top of it to keep it from falling into the wrong hands and the keys given to each member of the Jedi Council, but now they are long lost and the Jedi Council itself has begun the search for them The Council, will consist of the former party members from games 1 and 2 such as Atton and Juhani and light sided players will locate them and help them acquire the keys and dark siders will hunt down and kill them before they can claim the keys.
At some point though, similar to the revelation in KOTOR and the Enclave scene in KOTOR 2, you find out that Revan was not killed in TOR but fled, using an experimental/risky force teleport power which kept him alive but as a consciousness, scattered across the galaxy. Both sides intend to use the force nexus to bring him back together, but whereas the Jedi seek light-sided Revan, the Sith seek his dark persona of Darth Revan- both sides want to use him as the ultimate weapon, hence the Exile's involvement.
Once the keys are gathered, the player goes to the Jedi Temple to unleash Revan. A dark sider will have to assault the Temple to gain access and a light sider will have to defend it from a desperate attack by the Sith. As the battle rages, you are sent to unleash Revan and once killing the mentor character you didn't go with, bring back Revan. However things don't go to plan as Revan is back but with both minds trapped in his body. A Jedi then fights Revan who is being controlled by his dark persona and vice-versa for a Sith who fights good Revan and he is the final boss. The good ending shows your character and Revan leading the Republic to victory over the Sith and heading a new Jedi Order with the council now fully assembled, along with the ghost of the Exile. The dark ending sees Darth Revan and the player leading the Sith victory over the Republic and disspelling the ghost of the Exile.
I know its a very rough outline which I literally just plucked from my head whilst writing, but for those who read it, what do you think? I would have to include a main villan obviously and re-arrange canon.
