* AngstWhatAngst: In a series that is otherwise hardly stingy about angst, Luke and Seven are oddly chipper at the end of ''Against All Odds'', considering the Galactic Empire has risen again, conquered both galaxies, many of their friends and whole worlds died in the crossfire, and [[ArsonMurderAndJaywalking Luke is back to living on Tatooine]] with his new family.
* AssPull:
** According to ''Against All Odds'', Luke didn't really fall to the Dark Side, as his real personality was safely locked away within his mind, while his body was an EmptyShell that did the deeds.
** Halfway through ''Dawn of Forever'', the Oracle reveals that she has a disused-but-functional [[spoiler: Death Star]] at her disposal. Where did she get it from? It was a discarded prototype. While it's possible this is meant to be the [[spoiler: Death Star III]] from the old ''Star Tours'' ride, insufficient information is provided to be sure.
* BrokenAesop: The two trilogies each end in ways that come off as mutually-exclusive in what they're saying.
** [[spoiler:At the end of ''The Road to Unity'', which has devoted time to examining the cost of being a hero, Luke and Seven's retirement to raise a family is depicted in a positive light, despite the bittersweetness of how many lives were lost in the conflict. This is all rather spoiled, however, in that with the rebirth of the Galactic Empire and Luke's return to Tatooine, everything said heroes fought for has been rendered null and void]].
** [[spoiler:And then ''The Price of Unity'' has the opposite conclusion, that Sebastian Skywalker really is the one person who can unity the Galaxies and shall have to devote his whole life to it. While the trilogy does stick to its predecessor's ethos that heroes are flawed, fallible people beneath their reputation, it's hard not to feel it'd have been kinder of his parents to continue the damn fight instead of foisting this inhuman responsibility upon him]].
** Following from the above, it's never really made all that clear why Unity under the domination of a single leader à la Genghis Khan or Alexander The Great would be preferable or more viable than the humanistic ideals of TheFederation. The story itself notes that Alexander's empire fell apart after his death. Except, at the end of the day, no real reason is given as to why Unity would survive Sebastian. In effect, Unity was formed from the conquest of different races that have no motivation to work together, other than against a common enemy or out of veneration for a leader-figure who will eventually die. While ''Franchise/StarTrek'' and ''Franchise/StarWars'' may each be somewhat naive in their traditionally idealistic portrayal of people, the UtopiaJustifiesTheMeans mindset of the Unity Saga winds up feeling more out-of-touch than either of its inspirations.
* DracoInLeatherPants: Chuck's love of Benjamin Sisko is taken perhaps a tad too far in making Sisko TheChessmaster, and eventually [[spoiler: the one secretly inhabiting Palpatine's body]] after the Empire comes back to power. This gets particularly blatant when Leia, aware of the ruse, notes at one point that there is "no trace of evil" within the possessed [[spoiler: Emperor]]. While Sisko may not have been a ''bad'' guy per se, his whole point as a character in [=DS9=] was that of a ''Star Trek'' captain with a darker streak than previous series had depicted until then.
* HarsherInHindsight: Towards the end of the review of "[[Recap/StarTrekVoyagerS3E21RealLife Real Life]]", Chuck delivers a deeply personal and affecting speech in rebuttal to the episode's perceived {{Aesop}} that MiseryBuildsCharacter, about how even the fear of losing a child is a trauma no-one should experience. Thinking back to that review can be rather uncomfortable, when considering Sebastian's whole arc revolves around MiseryBuildsCharacter, including the loss of a child.
* HilariousInHindsight: The Unity Saga features several elements similar to the direction ''Star Wars'' would take after being bought by Disney, including a Sith Lord named Ben, who [[spoiler: develops a bit of a MemeticLoser status and eventually undergoes RedemptionEqualsDeath]], or the resurgence of the Galactic Empire.
** You have to wonder if Chuck didn't plant ideas in Rian Johnson or Alex Kurtzman's heads for the "deconstruction" of heroes, considering how the Unity Saga puts [[Film/TheLastJedi Luke Skywalker]] and ''especially'' [[Series/StarTrekPicard Jean-Luc Picard]] through the wringer.
* MoralEventHorizon: When Ben Skywalker kills [[spoiler: Jorielle Sunspring, who was pregnant at the time]].
* {{Narm}}:
** ''Franchise/StarWars'' and ''Franchise/StarTrek'' are both famous for their Narm-y dialogue, but the way the characters talk here frequently crosses over into a Joss Whedon-esque mixture of ironic self-awareness with a chance of angst, and the result can be immersion-breaking.
** Molly O'Brien doesn't take on a new name when she joins the Sith. Imagine facing a [[TomTheDarkLord Dark Lord called Molly]].
* RonTheDeathEater: Janeway's characterisation is similarly afflicted by the author's biases as Ben Sisko's entry under DracoInLeatherPants, albeit in the opposite direction, especially once she becomes [[spoiler: the Oracle]]. Granted, Janeway was always a [[BrokenBase controversial]] captain, but Chuck's narrative decision to follow his humorous interpretation of her as out-and-out evil and ''play it straight'' ends up erasing any nuance her character may have had.
** Ironically, the story appears to be aware of this and attempt to avoid having her look UnintentionallySympathetic; in ''Dawn of Forever'', characters note the one thing she wouldn't do is seek to destroy Earth, only for Janeway to push forward in trying exactly that, at which point it feels less like it is the Dark Side than the author pulling her strings.
* RootingForTheEmpire: A literal example, during certain parts of the series.
* StrangledByTheRedString: Luke Skywalker and Seven of Nine.
* TakeThatScrappy: When the Death Star II is complete, their first test is blowing up the Moon of Endor and the Ewoks.
* TheWoobie: "They're going to take it all away from you, [[spoiler:Sebastian]]." And boy, do they ever.
* TheyWastedAPerfectlyGoodCharacter: Kira Nerys is rather conspicuously absent over the course of the series, only mentioned by a throwaway line to have [[BusCrash died]] at some point between the two trilogies in a guerilla operation together with Miles O'Brien. Given that Kira is canonically a former freedom fighter, this feels like a pretty convenient way for the story to avoid addressing the implications of [[spoiler: Ben Sisko, her old friend and former commander]], leading the Galactic Empire in secret.
** Similarly, Odo's fate is never elaborated upon, despite the story dangling a pretty big RedHerring in the character of a Changeling working as head of the ISB.

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