As of Iokath, Acina or Malcom could be deceased and the decision made here decides who the leader of either faction is. Vowrawn steps into the breach left by a dead Acina while Malcom's demise leads to the infuriatingly faceless and voiceless Supreme Chancellor Jebevel Madon stepping down and allowing Galena Rans to succeed him.
The Nathema Conspiracy adds to this by setting up the eventual option for the facilitator of either of the changed outcomes to actually join the faction they potentially screwed over back on Iokath. Alternatively, of course, they could just continue on with their previous alliance and thus avoid any awkward outcomes.
This is a fair amount of variety that we could be seeing going forward, and this isn't even going into what else could be factoring into the factions' strength. This is something which BioWare have attempted to address with Nathema by reintroducing or introducing people who are or used to be important politically and killing them off for certain Classes. Given who some of these individuals are and how difficult it would be to align them with both the political status we've been given throughout KotFE and KotET and how they could severely impact a future balance, it's relatively safe to assume that all of these characters have been given a final farewell.
However, that doesn't mean that there still aren't questions and observations that need to be addressed. Be aware that every significant character a Class will face during the Nathema story will be mentioned here, so if you don't want to know who you'll face before you do, I advise you to stop reading here.
Before I start on the individual Classes themselves, there's a fairly important point that needs to be made.
Darth Mortis of the Dark Council is one of the six NPCs every character has a chance to see depending on their choices throughout Eternal Throne. In this case, he serves as the equivalent to Indo Zal should the Commander choose to be a benevolent ruler as opposed to a dictator.
The Dark Council is a peculiar beast to tackle, for one main reason. The only members of the Council known to actually exist by the time of Fallen Empire are Darths Acina, Marr, Mortis, Ravage, Vowrawn, and Imperious/Nox/Occlus. Acheron, Arho, Arkous, Baras, Decimus, Hadra, Soverus, Thanaton, and Vengean are all non-entities (if not deceased) by the end of the different Class, faction, and universally-accessible stories, and with the exceptions of Vengean, Baras, Arho, Hadra, and Thanaton we never learn who succeeds who. Soverus in particular is notable since we never learn which Sphere he represents and thus who he succeeds, while Acina herself succeeds Hadra's successor, Darth Karrid, who never appears in-game herself.
The point is, it's next-to-impossible to work out what the status of the Dark Council is even prior to Fallen Empire making it a non-entity and rendering everyone other than Acina and Vowrawn as missing, presumed deceased - the exception being Marr whose death is an absolute certainty. Mortis's survival, without even addressing this, is thus not very helpful and only raises the question of how Acina was able to create and hold such substantial power for herself with not one but two superior and more experienced Councillors still alive.
That said, Vowrawn and Mortis did always seem to be among the more prudent of the Councillors, so I can sorta see them letting her get away with it, especially as Mortis insinuates that he only takes exception to the Commander's rule of the galaxy due to their being weak. His being written back in, however briefly, still throws into sharp relief how little we know of the running of the Empire besides Acina being Empress, although the presence of thrones in the throne room beside hers implies that at least some form of Dark Council still exists.
Despite the fact that every Class sees someone different depending on decisions they made either during the Class story or on Iokath (although I still don't know what exactly factors into the Knight and Consular receiving a different option), that's not to say that they see someone important. Notably, the Hunter, Inquisitor, and Smuggler are greeted by wholly-insignificant characters to the galaxy in both cases, while the Consular, Knight, Trooper, and Warrior all meet with one character who is known to be politically significant. The Agent is thus the only character who meets with characters whose death is very significant, politically or otherwise, in both outcomes.
While characters like Master Sumalee, Darths Baras and Zash, and Khem Val are important to the respective Class characters, their deaths in this Flashpoint mean next-to nothing to the galaxy as a whole. Sumalee wasn't a member of the Jedi Council, she was just another Jedi - albeit one who had a vested interest in the criminal underworld and an effective strategist. Baras and Zash may have been ambitious as heck, but their political power was totally stripped from them by their apprentices with Baras even being disgraced and imprisoned if he is spared. Khem Val is easily the least significant politically here, despite his relative cultural significance, given his status as a bound servant to the Inquisitor.
Additionally, just because I consider a character non-crucial going forward doesn't mean that their appearance here doesn't raise questions. Baras above is a prime example, since despite his disgrace he's still likely to have attempted to make his voice heard over the years. Servant One and the actually-not-dead Sophia Farash aren't exactly crucial characters now that Vitiate is deceased, but the status of the Emperor's Hand and the Children of the Emperor is still something which would be very interesting to learn about following his death.
Servant One's appearance in this Flashpoint is especially interesting since he appears not before the Warrior but before the Knight; this is the first instance of a unique individual from one Class Story appearing in the unique conversation afforded to another Class. Previous characters who appeared cross-stories (Darth Lachris and Doctor Ianna Cel) used to be generic open-world NPCs who then became acquainted with one character later on (Consular and Agent respectively), but we've never had a unique Class NPC approach another by themselves until now.
More fuel for the "Fallen Empire/Eternal Throne is the Knight's Story" crowd.
It's not even worth identifying the individuals a Bounty Hunter, a Smuggler who took control of the pirate fleet, or a Trooper who aligned with the Empire on Iokath face on Nathema, although I will mention them for fairness. They're all new characters who are entirely insignificant outside of people simply seeking vengeance for the sake of certain individuals.
That's all there is to them as individuals.
Now we're getting into the meat of the matter; the characters whose appearance and subsequent writing out raises a fair amount of questions.
A dark Consular receives probably the most interesting, theoretically, of these characters: the Voss mystic Gaden-Ko. Immediately you should get some idea why I find this a very interesting scenario. The Voss are, of course, very high-minded and take the views of the mystics incredibly seriously. If a mystic takes enough of an exception to an individual that they're willing to help somebody kill them, that implies that a good number of Voss are willing to adhere to this viewpoint as well. Admittedly, the Consular is not directly responsible for Gaden-Ko's death and the Alliance has had the support of Sana-Rae for years so the Voss could simply dismiss this, but the point is that the Dark Side Consular probably wouldn't have won many friends on Voss by taking one of their mystics away and then eventually - albeit indirectly - leading him to his death. Depending on how much of a hold the Voss have diplomatically, this might also reflect badly on whichever faction said Consular allies with if - and only if - this route is actually pursuable.
A dark Knight (no, not that one) reconvenes with a formerly close ally in the form of Bela Kiwiiks. Kiwiiks is one of the only two Jedi Council members confirmed to be alive by the time of Fallen Empire, since Jaric Kaedan dies on Ilum and Tol Braga and Syo Bakarn could be killed by the Knight and Consular respectively but disappear from active service even if spared (Braga is later reported as deceased by the Star Cabal and an Imperial HK-51), while a Consular might never be invited to the Council depending on how they handled Syo.
The point is that much like the Dark Council we really don't know how the Jedi Order was running during the time of the Zakuul Empire, especially as the Grand Master herself, Satele Shan, disappears. With Bela as the next-most-superior Council member with the loss of Bakarn, Braga, and Kaedan, it is possible that she herself became the next acting Grand Master, but that's only a very unlikely hypothesis on my part. With her now potentially being written out of the story for all-time, an entirely new Council will need to be formed, maybe with a certain Kel Dor included.
I will get my Gnost-Dural fix in-game one of these days!
It is interesting to think how else this could impact certain matters. Bela of course used to be the Master of Kira Carsen and the first person to see and acknowledge Kira as more than she perceived herself as, forever earning the trust and respect of the former Emperor's Child. Bela's death at the indirect hand of the Knight could have a knock-on effect when it's time for a Knight who did interact with her to reconvene with Kira making it possible for her to walk away if the wrong things are said in the reunion conversation. I doubt they'd make it so that she walks away from a Knight no matter what, but then that's because I'm unsure what exactly leads to Bela appearing and every single reunion scene since Dorne, Quinn, and Temple only requires you to have just completed Eternal Throne and none of the additional story elements.
We'll have to wait and see whether that gets addressed.
While the Imperial character a Republic-aligned Trooper meets on Nathema is entirely insignificant, the same can't be said for the Republic character they meet should they have aligned with the Empire. General Elin Garza is apparently reinstated into active service regardless of what the Trooper decides on Rishi (this doesn't seem to be addressed) and derides the Trooper as a disgrace to Havoc Squad due to ignoring the sacrifices made by the Republic and aligning with the Empire. Ignoring the hand-waving of her fate on Rishi, this is easily one of the more logical outcomes of the sixteen Class-specific ones, since Garza of course would never take this lying down.
I'm counting this one as significant due to the aforementioned implication that she's still working in Special Forces. After all, she's still wearing her uniform. While her significance to Special Forces is essentially a non-entity after Rishi, it's still important to note that Special Forces is yet another one of those organisations whose continued operation is something of a mystery; the only squad known to be operational at the time of Fallen Empire is Havoc Squad, and they promptly joined the Alliance and lost all but two of its members. Heck, perhaps even all but one of its members!
Since we'll be going back to war between the Empire and Republic, the military of both factions is something which we're going to be seeing an awful lot of, so hopefully we'll get some more exposure on Special Forces and - although I'll be discussing this in a bit in this post - the SIS.
If a Sith Warrior kills Darth Baras (and it doesn't bug out so that a zombie Baras appears), they learn that Darth Mortis isn't the only Dark Council member to have survived alongside Acina and Vowrawn. Darth Ravage rears his judgemental head once again and takes issue with the former Emperor's Wrath for going on a "rampage for justice".
While I hand-waved Mortis as allowing Acina's rise to power due to him probably seeing and acknowledging her strength in the position, I can't do the same for Ravage. This is the same person who dismisses both the Inquisitor and Wrath readily due to their lack of experience and power, especially in comparison to his fellow Councillors. Acina is not only a less-experienced Sith and Councillor compared to himself, but she's also made mistakes in the past; it was under her watch, after all, that the Dread Masters broke into the Arcanum facility - not once but twice - and stole precious and dangerous artefacts and it's not even guaranteed that she was the one to fix it all.
Additionally, compared to some of his fellows, Ravage truly is the archetypal Sith: ambitious, cunning, and sneering. It is exceedingly unlikely that he would have easily been brought to heel by anyone other than Marr, even with the threat of Zakuul looming over them all and equally as unlikely that he would actually have sought out a third party to eliminate someone who he personally sees as a direct threat. Additionally, since he's pissed off both the Inquisitor and Warrior it is rather aggravating to see him be given a very backhanded death without any direct input even from the individual who gets to chat with him.
I'm going to end with the Agent since, as mentioned, both individuals they meet are rather significant somewhere along the line.
If the Agent spares Ardun Kothe and eventually agrees to become a double-agent, they are confronted by Shara Jenn - the former Watcher Two and second Keeper in the Agent story. Much like Garza before her the Rishi story had made her something of a non-entity - moreso than Garza, actually, as she's given the chance to escape from the Empire as she has her loyalty programming undone - and again it's frustratingly hand-waved.
Alternatively, should the Agent remain loyal to the Empire even if they spare Ardun Kothe, Marcus Trant - the Director of the SIS himself - will appear. He mentions that the former Cipher is being treated as the third-highest threat to the Republic (even after taking control of the Throne? I'd hate to meet the other two individuals...) and to this end he has taken advantage of the chance to eliminate such an important adversary himself.
Both outcomes throw into sharp relief that, once again, the organisations both characters represents are rather problematic since we don't know all that much about how they are being run at this moment in time. Considering that Shara represents Sith Intelligence, the organisation that both Cipher Nine and Lana Beniko were also a part of before the whole Zakuul escapade, this is exceedingly aggravating. Jonas Balkar at least got a mention in Fallen Empire (admittedly only for Troopers, but it counts!), but this is the first instance of someone from Sith Intelligence who isn't Lana Beniko or Cipher Nine themselves being identified directly. What became of Watcher Three, the various Fixers, and the new experimental Watchers? Are they still kicking around or have they been given the Watcher-Two-Rishi-treatment?
While the rushed deaths of all of the previously-established characters is disappointing, none are anywhere near as disappointing as the treatment of Marcus Trant. Trant, for the uninitiated, is one of the most-established of all characters in the SWtOR lore, having first appeared in the Lost Suns comics way back in 2011 before the game even launched. His appearing in-game was thus severely overdue, especially as he's been mentioned a couple of times by Theron Shan himself. To see him appear in-game at long last and then instantly brushed aside is, in my eyes, nothing short of an insult to the character and especially his history with Theron.
That said, Trant's subsequent potentially being written-out from the story entirely might pave the way for Jonas Balkar to become the new director of the SIS should the organisation get the chance to feature again. The same can't be said of Sith Intelligence, simply because its only identified director left to become a founding member of the Alliance and the main candidate for replacing her is now more-than-likely gone for good. Maybe this is the meek Watcher Three's chance to shine?
Going forward, one thing that I hope the story doesn't do is try and shake things up even further. There's a lot to be said for a state-of-permanence, and hopefully writing out some of the more obviously-confrontational characters such as Ravage (as much as I disagree with the execution) will help to achieve this. That's not to say that there still won't be opportunities to have confrontations within the chosen faction, but they should hopefully be minor and negotiable.
This is perhaps the only way I can think of justifying Marcus Trant's being written out entirely, since his history and close relationship with Theron - closer in many regards than that of Satele and especially Jace - would make it next-to-impossible to get in his good books if Theron dies. We already know Satele's justified view on it, and it's likely that while Jace and characters like Jonas will take some exception to it they'll also be able to understand why he could be left to die. Depending on how closely a surviving Malcom views the Alliance as an ally to the Republic, it's probable that he'd take Theron's 'betrayal' - especially since he already views his leaving to join the Alliance as one - very poorly indeed.
I do sincerely hope that we get more than a little bit of exposure on the running of the various organisations. The Jedi and Dark Councils in particular are of close interest to three of the Force User player characters, while the military and Intelligence aspects would of course appeal to the Trooper and Agent. For all Classes the political status is something that would be especially useful to learn about.
Maybe we'll actually get to see Madon for a change. Unless they decide to write it so that Madon and Acina step down (or get assassinated or whatever) so everyone gets Rans and Vowrawn as the leaders regardless of their choice on Iokath. That would certainly help alleviate the awkwardness of every player potentially seeing a very different galaxy depending on one moment on Iokath which any potentially-instant-Level-70s would never get to see, although it would still count as "shaking things up" a fair amount.
Heck, even Malcom could be written as stepping down due to the stress of the job so that everyone who joins the Republic meets a new Supreme Commander. Chronologically, he has been in the position for about ten years now, and he's not exactly a young man anymore...
Regardless of what happens, I'm looking forward to seeing where the story takes us. More than anything, I'm excited to see what any potentially new open-world planets are like following the amazing scenery present in Copero and the reborn Nathema in particular. The story has improved substantially since Iokath last year - in spite of the various questions Nathema raises for certain individuals - so hopefully it continues the current high-standard we've been seeing.