* DarknessInducedAudienceApathy: Killing off [[spoiler:Kathryn Janeway]] in ''[[Literature/StarTrekTheNextGenerationRelaunch Before Dishonor]]'' and wrecking much of the Alpha and Beta Quadrants in ''Literature/StarTrekDestiny'' (along with [[BittersweetEnding even more losses]]) was [[WhamEpisode pretty serious stuff in its own right]], but the Trek novel universe has proceeded to [[SlidingScaleOfIdealismVersusCynicism veer quickly and deeply]] into CrapsackWorld territory with [[spoiler:the destruction of Deep Space Nine and the Bajoran Wormhole]] in ''[[Literature/StarTrekTyphonPact Typhon Pact]]'' and [[spoiler:the gradual collapse of the Federation]] as of ''[[Literature/StarTrekTheFall The Fall]]''. The ConflictBall and AppleOfDiscord now [[RuleOfDrama fuel the novel series]] to [[OnlyTheAuthorCanSaveThemNow such an extent]] that the AlternateContinuity of ''VideoGame/StarTrekOnline'', for all of its own [[ForeverWar constant warfare]], is actually LighterAndSofter by comparison.
** As an alternative view, [[spoiler:Janeway]] returned, the [[spoiler:wormhole]] reopened, Bajor is a powerful and prosperous Federation member, a second more advanced [[spoiler:Deep Space Nine]] replaced the lost one, the same devastating conflict in ''Destiny'' also liberated the Borg and freed billions from oppression, and in doing so removed the biggest blight to Trek 'verse civilization, the Federation has held together, rebuilt and reaffirmed itself in spite of everything, and inspired the Typhon Pact nations to start to overcome their histories of xenophobia and isolation on top of that, the Andorians are cured of their genetic problems, the Cardassians and Ferengi have the best governments they've ever had and are now official allies of the Federation, the Romulans have a moderate and diplomatically adept government, the Federation has slipstream drive and is penetrating all four quadrants, and Starfleet is starting to turn back to exploration again. Also, political instability and uncertainty isn't, others might say, anywhere near "CrapsackWorld" - especially when war has been consistently avoided (Borg aside, and they're more a force of nature than a nation).
*** In short, an AuthorsSavingThrow, for now. However, at the very least, that moderate and diplomatic new Romulan government is going to get [[OutOfTheFryingPan torn to pieces]] as soon as the Novel Verse's continuity catches up to [[Film/StarTrek the Hobus supernova destroying Romulus and Remus]].
** Torvig Bu-kar-nguv of ''Literature/StarTrekTitan''.
** President Nanietta Bacco, who went from a "the president resigned last book so we need a new president" character to a popular character carrying her own West Wing-style political novel, ''Literature/StarTrekArticlesOfTheFederation''.
* FridgeLogic: One of the more infamous is the desire to make sense of the Tamarian language from ''Darmok''. A very popular episode, but great amounts of FridgeLogic result, for the books to eventually deal with. For example, how do the children learn the legends? Answer: Probably not unlike how Chinese speakers learn the [[TranslationYes four word idioms]]. English too has plenty of strange expressions with obscure origins, but speakers understand the meaning from the context. In fact, the metaphorical meaning tends to become the ordinary meaning over time; for example, English "understand" no longer refers to standing under anything but has become a dead metaphor. Or perhaps the children are taught the stories via some visual medium, like movies or plays.
** FridgeLogic #2: To build starships, one needs language more precise and less ambiguous than metaphors. But this too is [[AllThereInTheManual all explained in]] the ''Star Trek Novel Verse''. Tamarian mathematical and musical notations are very closely linked. Tamarian engineers and programmers sing equations, transferring instructions through music. Even in ordinary speech, numerical information can be conveyed through the pitch of a Tamarian’s vocal harmonics, though it can be hard for untrained Human ears to discern the nuances, just as it can be hard for an English speaker to learn to hear Chinese tones.
---> "This answers the infamous question one linguist posed to illustrate the apparent limitations of Tamarian as a practical language: “Mirab-his-sails-unfurled factor what, sir?”
** FridgeLogic #3: Why the universal translator even translates their language in the metaphorical way in the first place, when we know the UT works on some kind of technological telepathy. If when they say "Darmok and Jalad at Tanagra" they mean "alliance", then why doesn't the UT just translate it as "alliance"? Answer: It wouldn't work in real time. "Computer: Cross-reference: Darmok, Jhillard, Tanagra." Computer tells the story, they go "Ah!" This would resemble the footnotes commonly seen in anime subtitles (see case 3A under TranslationStyleChoices). But explaining Tamarian legends to a foreigner is a slow process. And besides, it loses the more subtle information about what ''kind'' of alliance is meant: in Tropese, it'd be close to EnemyMine.
** It even loops right back around to FridgeBrilliance: English "set" has over a hundred meanings distinguished only by context, and Mandarin Chinese can be just as bad with its homophones and [[TranslationYes four-word idioms]]. Likewise, there's so many possibilities for a particular Tamarian phrase, it requires an incredible intuition to determine the intended meaning, one normally honed through a lifetime of speaking such a condensed form of language. The universal translators are notorious (DependingOnTheWriter or perhaps the make and model) for having difficulties with some of the more 'quirky' or abstract parts of languages.
* NightmareFuel: The [[OmnicidalManiac new]] [[RoaringRampageOfRevenge and]] [[KillAllHumans improved]] [[AxCrazy Borg]].
-->''We are the Borg. You will be'' '''annihilated.''' ''Your biological and technological distinctiveness have become irrelevant. Resistance is futile...'' '''but welcome.'''
* TearJerker: Hadlo's death. [[spoiler: "Oralius! Prophets! My love is for you both!"]]
** [[spoiler: Owen Paris' last message to Tom in Literature/StarTrekDestiny]].
** [[spoiler: Kieran Duffy's death]].
** [[spoiler: Garak: "There is no home anymore! Can't you see, its gone!!"]]