Franklin Drake essentially inherited the preexisting argument about Section 31 (see YMMV.Star Trek Deep Space Nine for details). Is he a Necessarily EvilPragmatic Hero with the Federation's best interests at heart, or a vigilante who takes stupid risks and gets Starfleet personnel killed and makes moral compromises for no good reason? In particular the latter camp notes the A Million Is a Statistic treatment of the Starfleet Intelligence and naval forces killed due to his actions over the course of the KDF House of Torg Story Arc, noting that if Section 31 really did have the backing its defenders ascribe to it, it would've been simpler and less costly to just tell Worf what was going on through normal channels.
According to later missions in the game, especially "Surface Tension", the main reason for the Federation-Klingon War is that the Federation is heavily infiltrated by the Undine. However, in the KDF storyline the Undine aren't even mentioned until you get to the "Cloaked Intentions" episode (where the Fedside fiasco on P'Jem gets a throwaway mention while you're decoding some Tal Shiar files). Couple that with the war having actually started when the Klingons decided to return to their conquistador days and started attacking Federation colonies, and the fact that J'mpok had been agitating for war with the Federation since 2387, and one starts to wonder if the Undine infiltration isn't really just a convenient Pretext for War. Even if you accept that the Klingons really were after the Undine in the Federation's ranks (as "Surface Tension" suggested), it's hard to argue that their actions were anything but utterly counterproductive, especially after they pulled the exact same damn stunt as with the Gorn in the lead-up to the Dominion War, were completely wrong that time, and drove the Cardassians right into the hands of the Dominion in the bargain.
Is J'mpok the Big Good, Big Bad, a Big Bad Wannabe, or a Noble Demon? He invaded multiple species, killed Martok in a suspicious duel, and waged war against the Federation that weakened the future Alliance before real enemies came calling. He's also helped numerous weaker species, led the Klingon Empire through the worst crises in its history, and reluctantly gone against his own allies on matters of honor. It seems that he wants to be the Big Bad but is a Pragmatic Villainy engaging figure who knows when there's a bigger threat. The issue is finally settled in "House Divided" with J'mpok firmly settling on the side of being the Big Bad. However, now there's the question of whether he was always this or whether he was driven to this by J'Ula's machinations as well as the loss of face he suffered during the Hur'q war thanks to Martok.
Is Martok the Big Good that he was when he was Chancellor, ready to save the Klingon Empire? Or is he a shadow of his former self that is aware that capture is the worst dishonor a Klingon can suffer? The fact that he is ready to fight House Torg, the Tzenkethi, and then the Hur'q is all a sign that he is still the warrior he used to be. However, he also acknowledges that J'mpok is the rightful Chancellor, which has left him Broken Pedestal for many Klingon players. He might also assume he has to be The Atoner for his failures. Like it or not, J'mpok has also led the Klingons through more crises than Martok did during the Dominion War. There's also the question of whether or not Martok's refusal to step up to be Chancellor despite J'mpok's actions is motivated by something other than not wanting to do the job. He has the Sword of Khaless and the pedigree to retake the throne but never even suggests that it's a possibility even when it's obvious the current one is unfit.
Was Worf siding with the Klingon Empire during the Federation-Klingon War the right decision or not? The fact it is the exact opposite choice to what he did during the invasion of Cardassia over similar justifications (invading because the enemy's leadership was subverted by changelings) is notable. Is it because Worf has a family in the Klingon Empire now or did he believe it was more important to be a moderating influence on the Klingon High Council?
Is Kahless II a General Failure and Clone Degeneration that never should have been put in charge of anything, let alone the Klingon Empire's version of Section 31? Or is he a Messianic Archetype that died in a Heroic Sacrifice? He was a figurehead Emperor that Worf indicated was something of an embarrassment but generally harmless. Yet, it was Kahless II who led to the defeat of the Fek'lhri as well as forged the Shard Sword of Kahless that the player character very likely used for many adventures afterward. He died at the hands of an Iconian but distracted it long enough for the player characters to find out their weakness. Generally, players think of him as an idiot but his actions worked quite well against the Klingons' old enemies.
Is Captain Kagran a General Failure and Ungrateful Bastard who sides with J'mpok against you in "House Divided" or is he Just Following Orders? He gets most of the United Fleet vaporized trying to fight the godlike Iconian fleet head on and has some ridiculous time travel plans. He is one of the few Klingons who doesn't put Honor Before Reason, though (until he does, again, by siding with J'mpok).
Is Captain Koren a Spoiled Brat or A Mother to Her Men? Despite being the captain of the Klingon Defense Force's flagship, she constantly pouts and throws temper tantrums when things don't go her way. She's also lacking in great victories to her name. Her bitching about the Federation not sending more ships to help defend Q'onos really cements her as an unreasonable whiner, considering she doesn't take into account the fact that Starfleet just fought off an Iconian invasion of Earth, one which almost crippled the fleet along with ESD.
J'Ula is someone that either goes through some considerable Character Development, suffers Chronic Backstabbing Disorder, bad writing, or just has Blue-and-Orange Morality. She is the sister of T'Kuvma but also a member of House Mokai so she's a scheming stealthy Klingon as well as The Fundamentalist. However, somehow she ends up working with the Federation as well as other races to try to overcome J'mpok despite that being the antithesis of her brother's vision. Does she develop some respect for other races or just hates him that (and his ally Aakar) much?
Is Aakar really THAT bad of a Klingon? Yes, he posseses a weapon that will result in Earth-Shattering Kaboom for his enemies and uses political subterfuge but that's what House Mokai does. Many players hated J'mpok and J'Ula BOTH, though, and note that Aakar may be better qualified to be a Chancellor than them (even to the point of wishing they could side with him). Robert O'Reilly's popularity certainly helped with his support from the players, though.
Romulans
Is D'Tan a genuine reformer who is doing what he feels is best for his people and honestly wants friendship with both of the remaining Alpha/Beta Quadrant superpowers (the official interpretation), a traitor to the Romulan way of life, or a particularly shrewd manipulator who is Playing Both Sides to improve the Romulans' situation?
Roughly the same debate plays out regarding the Romulan Republic as a whole. Some hate them and call them "space hippies" for wanting to coexist peacefully with their neighbors rather than being the scheming villains we saw in the Star Trek: The Next Generation-era shows. (The Republic military plays more towards the honor-bound soldiers portrayal of Star Trek: The Original Series, and Cryptic used Diane Duane's Rihannsu worldbuilding extensively.) Others point out that among other things, hippies don't arm ships with thalaron generators. And then there's the guys that are just openly Rooting for the Empire and want to join the Tal Shiar. This got worse with the release of "Uneasy Allies" and revealing that there were still Imperial loyalists not even connected to the Tal Shiar still around.
Subcommander Rai Sahen, a Romulan Republic Intelligence operative who turns up for a few missions in Delta Rising, has been accused of being a Tal Shiar mole for picking sneakier, more stereotypically Romulan solutions to various diplomatic problems (the big one being "Operation Cooperation Conspiracy", a Genghis Gambit she pulls on the Benthans and Hazari by attacking them with a captured Vaadwaur ship in a False Flag Operation). On the flipside, the same mission has the occasional fan asking for dialogue options to wholeheartedly approve of the mission, especially if they're playing a Romulan (the existing options are three variations of What the Hell, Hero?).
Is Slamek really just Hakeev's mole, or does he help the PC hoping that they can actually succeed and get him out of being a prisoner in the Coliseum? He does actually get within an ace of being rescued along with the PC; it's only Hakeev's last-minute appearance that foils it. (Then again, Slamek is The Woobie who was first abducted by the Elachi, then experimented on by the Tal Shiar, prior to being captured by Hakeev; so he may have finally broken and decided his only chance was going along with his captors, even when it meant risking his life in the arena.)
Does Hakeev actually care about capturing the PC, or is he more interested in breaking what little spirit Slamek has left by this point? There are numerous chances to catch the PC during the escape, especially since it's known where they are going. Maybe the real purpose is to give Slamek a glimmer of hope and then snatch it away at the very last minute.
Delta Quadrant
The apparent developer intent of the Kobali/Vaadwaur conflict was for Space Nazis (Vaads) to be preying on a friendly but mildly misguided alien race (Kobali). The general player perception of the arc is Designated Hero (the Kobali) versus Designated Villain (the Vaads). The Vaadwaur are a nearly extinct species presented as Scary Dogmatic Aliens, but are shown to have had their upper echelons parasitized by bluegills except for their leader Gaul, suggesting they wouldn't willingly have gone along with his plans. Meanwhile the Kobali basically reproduce by necromancy and rarely seek the consent of the people they resurrect and convert into Kobali, which has drawn comparisons to rape by players. The revelation in "Dust to Dust" that the Vaads prioritized their children for storage as Human Popsicles, which the Kobali have been using as reproductive stock, only made this worse.
Based on what the Talaxian extras are doing in "Reunion" (sitting around drinking, trading shifts to the point where nobody knows who's supposed to be on duty when, leaving spices lying around all over the place, etc.), jonsills and worffan101 reinterpreted Neelix as the Only Sane Man among a race of slackers (to the extent where he's sincerely trying to be helpful and just isn't very good at it).
Pre-Delta Rising, it was observed by some players that the Undines' stated motivation (attacking the Alpha/Beta Quadrant nations in revenge for their apparently breaking the truce negotiated by Captain Janeway in "In the Flesh", which was really an Iconian False Flag Operation) doesn't actually make sense: if the Undine infiltration was really as extensive as is claimed in-universe, they should have figured out by now that no such attacks were ever actually ordered. So either the infiltration is not as bad as claimed, or the Undine just used the false flag attacks as an excuse.
