Hear me out. Knights of the Forgotten Empire but...
Valkorion is alive. And your characters are broken out of Carbonite for different reasons, based on their class.
1. Imp Agents' and Troopers' mission is to create and lead teams whose job is to infiltrate/storm high security stations like Star Fortresses and Experimental Weapons labs. They have a plot involving a highly disaffected Arcann, who is done with his Father's shit. This may or may not lead to a romantic relationship, based on player choice. Conversely, Agents can have a story about showing the ppl of Zakuul how evil Valkorion is, turn them against him, while leaving the "storm the bases" quests purely to the more overt Trooper.
2. Bounty Hunter is broken out on the condition that they work exclusively for the Alliance now. Undertake jobs to hunt down Zakuulan collaborators and VIPs. Usually some small story changes when taking them alive or eliminating them.
3. Similar for the Smuggler, but their job is more related to movement of goods (i.e. Smuggling) than people (though that can be done too: transporting commando squads to high risk zones). Perhaps they have the Arcann plot too.
4. Consulars and Inquisitors are deployed against Vaylin, Scions, Nathema Zealots, and the like. They research rituals, aimed at ending Valkorion's Immortality maybe but also other sinister dark magicks. Vaylin is trying to break free of Valkorion, but not necessarily for anyone's benefit but her own. Consulars and Inquisitors can help her, if they choose, maybe grow close to her and earn her trust. Perhaps a love story, or even a tragic love story.
5. Knights and Warriors are their usual, generic selves. Taking names and kicking ass. They lead frontal assaults, mostly, and face the more Frontline divisions like Zakuul Knights, Exarchs, Paladins, Horizon Guard, etc. Perhaps they are the ones who take on Valkorion. They might face Vaylin and/or Arcann in battle at some point, and even win though not necessarily kill them. Love interest option here too. Yeah, it's true I'm partial to both of these direct, melee-oriented classes, but let's face it, these glamorous adventure stories are what Knight and Warrior are known for.
All class stories end with Vaylin and Arcann joining the Alliance, and with the final slaying of Valkorion and it is like the mission to kill Revan Reborn. By this I mean that everyone who lives participates: Lana, Theron, Satele, Shae Vizla, Senya, Arcann, Vaylin, etc. (I belong to the "Ordinary folk should not be able to face the strongest Force-wielders in the Galaxy" school).
My mental image of how a super strong Force user would fare against regular people. Pics from Star Wars: Vader Down
Ahem. Went of on a tangent there, sorry. Moving back. It's at this point that Arcann and Vaylin can be killed/die from circumstances, with special dialogue depending on the classes.
The Alliance leader's identity is a secret, revealed at the end to be either Supreme Commander Jace Malcom for Republic Players, or Admiral Zasha Ranken for Imperials.
