* During the Mission "What Lies Beneath" the player is trapped in a [[CreepyBasement small, poorly maintained part]] of Drozana Station with practically no lighting. [[JumpScare Then, out of nowhere, you hear...]] '''''[[http://www.youtube.com/watch?v=rq4dyIbP6NQ this.]]'''''
** For those who don't want to listen: [[JumpScare Bonnie-kin, Bonnie-kin,]] [[ParanoiaFuel I see you.]] Bonnie-kin, Bonnie-kin, what will you do? [[JumpScare Bonnie-kin, Bonnie-kin,]] [[RedShirt dress all in red.]] [[NightmareFuel Bonnie-kin, Bonnie-kin, soon you'll be dead!]]
** It's not much better when you learn ''what'' the source of the creepy gloating is--[[spoiler:It's a HardLight construct (read: "Hologram") working in that CreepyBasement you're stuck in, driven mad by the [[EnergyBeing Devidians]].]]
** [[spoiler:'''[[VillainousBreakdown THEY]]''' [[VillainousBreakdown sent you, didn't they, my little Bonnie-kin? To halt my]] '''[[VillainousBreakdown WORK!]]''' [[VillainousBreakdown To change my]] '''[[VillainousBreakdown PROGRAM!]]''' [[VillainousBreakdown You'll not survive to perform such tricksies, oh no, my little Bonnie-kin...]]]]
* During the Tie-In novel, ''The Needs of the Many'' we get treated to understanding what it is like to be an Undine infiltrator. Unlike the Changelings of ''Series/StarTrekDeepSpaceNine'', the Undine don't just copy your body, they copy every part of your body including your internal organs and ''how your neurons fire in your brain.'' This means they don't just copy you physically, they ''copy your '''soul'''.'' Worf in particular had to deal with this threat after he was injured in a battle and Undine tried to replace him, but due to his injuries he had a memory lapse during the struggle and the next thing he remembered was seeing himself be thrown into a Vulcan body disintegrator (a means of disposing dead bodies since the Katra is what matters, not the body). For the next 30 years Worf is horrifying confused as to whether he's Worf, Son of Mogh or an Undine who believes he's Worf and that the Worf personality overwrote his Undine one so thoroughly that he's just complete fake. Jake Sisko notes that he can blatantly see '''TERROR''' in Worf's body language. The worst part is, for a GenreSavvy reader, who's full aware of the [[TheWorfEffect trope that Worf made]], you know it's highly possible that this ''is'' an Undine who thinks its Worf. The ParanoiaFuel of this concept literally is what made the game and the entirety of the STO universe bloody terrifying.
** ''Slightly'' downplayed in one the game's missions: the Undine still need regular injections to maintain their assumed form, so there is a relatively easy way to test it if you think you might be an Undine, assuming you have time and reliable allies that you think aren't Undine.
* In Colosseum, a mission in the Cloaked Intentions story arc, you return to your ship from a fairly easy away mission [[spoiler: and wake up in a prison run by brainwashed Tal Shiar working for the [[TheManBehindTheMan Iconians]].]] You're left to wonder how you ended up in this predicament when during your [[spoiler: escape from the arena]], you see it. [[spoiler: An [[AbusivePrecursors Iconian]] gate. And you realize how you ended up in their arena, they just walked into your quarters or your ready room and took you. The [[BigBad Iconians]] can literally just kidnap you without anyone ever knowing and take you somewhere no one will ever find you. Pure ParanoiaFuel.]]
** It's more implied they intercepted your transporter beam, but the paranoia remains.
* The bad future in the timeline created by the Enterprise-C's jumps to the TNG and STO era. First, the Feds lost the war but continued to fight guerilla warfare. However, at the same time, a Bajor that was never conquered by the Cardassians discovered the Wormhole and the Dominion swarmed in. With no Starfleet, Section 31 or The Sisko to stop them, they cubstomped the KDF and Romulans and destroyed Earth. The Tholians were spared by signing a non-agression treaty (as seen in ''Series/StarTrekDeepSpaceNine'') and control Tau Dewa where the player and their starship is now a freighter serving the Tholians. Along the way you meet your 3 most senior Bridge Officers who are run down people who never experience joy in their lives, and meet many of your friends from other STO missions. It says something when Admiral T'Nae, a Vulcan, doesnt even bother being coldly logical anymore and blatantly emotes depression. And to add some FridgeHorror to the mix, because the Romulans were defeated, the Iconians never destroyed Romulus, which means the JJ Timeline ceased to exist. Yes, that's right. The Enterprise-C's time travel adventure nearly caused TWO timelines to face non-existence.
* With ''Legacy of Romulus'', we get a new look at the [[spoiler: Elachi]]...and it isn't pretty. [[spoiler: It turns out that they are trying to convert Romulan colonists into creatures like themselves. [[BodyHorror The results]] are anything but pretty and anyone you cannot save [[MercyKill you decide you need to destroy to be merciful]]]].
** For bonus points with FridgeHorror. [[spoiler: all those Elachi you killed? They could have been your friends and family from your colony. Though it was probably a MercyKill.]]
** And it gets even worse: [[spoiler: converting those poor colonists into creatures like themselves? ''That's more-or-less exactly what the'' '''BORG''' ''have been doing'' - '''you're simply fighting biological vampires instead of half-mechanical zombies.''']]
* One mission in the Romulan faction, Mind Game [[spoiler: forces your captain to undergo Tal'shiar mental reprogramming. You ''can'' resist, but the [[GoodAngelBadAngel will of Empress Sela drowns out your first officer]] and [[ButThouMust in order to continue]], you have to do [[UnwillingRoboticisation some]] [[KickTheDog pretty]] [[FaceHeelTurn awful]] [[PlayerPunch things.]] The worst part is, even if you try to resist, Sela just tells you some reason you can't. [[MindRape Mind Rape]] at its worst.]]
* The first mission of "Undine Advance" (formerly the Undine Front) is merely called "Assimilation", where your Federation captain investigates some unusual Borg activity. [[spoiler: There you find out the Borg have '''assimilated some Undine''', something once thought to be impossible.]] OhCrap.
** At least we stopped them before the knowledge could be transmitted. ''But there's nothing saying it can't happen again...''
* Fighting the Borg is always pretty scary, especially if it's your first time since the tutorial and you've forgotten to acquire [[AppliedPhlebotinum frequency remodulators]]. Few things are more OhCrap inducing than a wave of Borg advancing on you when your weapons are having ''absolutely no effect''.
** The first time one of your away team gets assimilated is also rather horrible. One of your own team, someone who may well have been with you since the tutorial, is now advancing on you with bits of Borg-tech sticking out of their head and there's nothing you can do about it but ''shoot them into unconsciousness''. Fortunately, you can then revive them as usual, but it's not a pleasant thing to have to do if you've [[VideoGameCaringPotential gotten attached]] to your away team.
* The Featured Episode "Sphere of Influence" [[spoiler:Thanks to dumb luck and disaster, you've tossed yourself into the ''Iconian Gateway System''. Even worse, there's evidence that they've been watching ''everyone'' - the Federation, the Klingon Empire, the Romulan Republic, the Dominion. You've found their plans and what they want to do with everyone, including wiping out everyone in the Sol System, wipe out the Romulans (with the hint that they may kill Empress Sela if they can't brainwash her) and when everyone's conquered, head for the Dominion and destroy them, too. ''They even have gateways in the Delta Quadrant''.]]
** Even worse, that disaster that dumped you there? [[spoiler: ''Their fault''.]]
** And worse than that? [[spoiler: Them having well explained reasons for ''why'' they're taking each action. The Sol System and Humans? Too creative and hate captivity (in a nice CallBack to The Cage). Klingons? Well they're warrior society has already turned everyone into a walking soldier and ease of taking orders: take control of the Great Houses and install puppet leaders and control them that way. The Romulans? Tried it once, didn't work out. We underestimated them. Not this time, ''eliminate them'' OR get Sela pacified in captivity and send her back as a new Hakeev. The Dominion? Both sides are fighting to a stand still. Do what the Dominion failed to do and take the Alpha and Beta Quadrants and use the resources to take them out (which says everything about [[WellIntentionedExtremist the Dominion]] in hindsight). The Kelvans? Stick some gateways in Andromeda and keep them busy and out of this. Once everyone's pacified and the Iconian Empire rules again? Make the servant races terraform the homeworld back to it's native beauty in the cosmic equivalent of making the dog smell his own duty on the rug.]] ''Damn.''
** Just the concept of [[spoiler: the Iconians having a massive foothold in Andromeda is scary. Prior to this, if shit got really bad and we had to leave the Milky Way, it was implied they couldn't follow via gateway. Looks like that's not possible anymore, the universe is their oyster and they ''will '''hunt us down.''''']]
** Hell, the [[spoiler: Iconians used to come to Earth to spread plagues and internal strife for study on us since the ancient past.]] ParanoiaFuel for RealLife.
** Yet another reason to be paranoid? [[spoiler: ''The Iconians have fingers in'' '''everything that's happened in STO''': from inciting the Undine's attack, causing the Klingons to go to war with the Federation, getting the Tal Shiar and the Elachi to kidnap races from all over the galaxy for study, and so on. And soon we might add the Voth to that list too.]]
* Speaking of [[spoiler:the Voth]], the ending to "Sphere of Influence". What's on the other side of that Iconian gateway? If you said the Dyson Sphere, you haven't played the mission. [[spoiler:There's an Omega Molecule on the other side. A threat so horrible that the Federation tosses out the Prime Directive and goes in guns blazing to destroy it. This is the equivalent of a WMD and if someone else gets a hold of it...]]
** Actually the [[spoiler: Omega Molecules]] are ON THE DYSON SPHERE. [[spoiler: It's a system-sized manufacturing facility. It makes everything from toys to Omega Molecules. The ''Voth are trying to claim them.'']]
** The Dyson Rep makes this worse. [[spoiler: The first Rep cutscene is a message from a rogue Voth scientist. The Voth have encountered evidence suggesting the Iconians are '''''in the sphere RIGHT NOW!''''' His government is covering up due to the doctrine and attacking the Joint Task Force to be a distraction. Even worse, occasionally you're attacked by Iconian Probes or Solanae Swarmers in the Sphere. They're here. '''NOW.''']]
*** Or those could just be still-functioning defenses from when the Sphere was built. Better hope it's that.
* At Tier 3 of Dyson Reputation you learn a bit more about the Solanae. You know how they're made of Solanagen? A material that can't exist in real space? And how subspace really isn't a habitable environment regardless? [[spoiler: They're not naturally made of Solanagen. They're from our galaxy, built that dyson sphere and then it [[GoneHorriblyWrong went horribly wrong]] altering the star and altering they're chemical composition. Imagine one day being so irradiated you stop being carbon-based life.]] Brrrr.
* Dyson Reputation Tier 5 has the ultimate WhatTheHellHero towards the Voth: [[spoiler:They want to weaponize Omega molecules for the express purpose of defeating a foe. They don't care if they end up isolating themselves or harming other races - they want to win, no matter the costs.]]
* "A Step Between Stars" gives us the frightening idea that [[spoiler:the Romulan Republic, the Federation and the Klingons might be on a collision course for an all-out war with ''each other'' over the new Sphere. And it's all thanks to the Undine.]]
** Another frightening thing? [[spoiler:The Undine can now waltz on into the Alpha Quadrant without opening rifts.]]
*** Well, supposedly. [[spoiler:That's what Tuvok says, but it doesn't actually make sense based on the other information available -- the Undine now have an easy gateway for their apparently massive already-in-normal-space fleets in the Delta Quadrant to the ''Solanae'' Sphere -- but the Solanae Sphere is in the Delta Quadrant, so the Undine would still have to get past the Dyson alliance-fortified (assuming the alliance holds) gateway to the Beta Quadrant (the gateway is in Romulan space)]].
** As well, despite the best intentions, it seems that D'Tan's dream of a peaceful Romulan existence may be nothing but a pipe dream, especially the way Commander Jarok was automatically willing to [[spoiler:claim the second Sphere as Romulan property. If not Undine infiltration, then it seems that the Romulans of New Romulus are just as power mad as the Romulans of the old Romulan Star Empire.]]
** That may be overreacting; if anything, the treaty New Romulus had with both the Federation and the Klingons likely helped end that old, bitter war by forcing them to work together in neutral space, and the Romulan people are no doubt acutely aware of all the help they've received. One ambitious general does not a power-mad society make. Also, you know. The Republic isn't torturing people, brutally terrorizing colonists into submission, threatening to drop thalaron weapons on their own people, conspiring with soulless monsters that convert innocent people into brainwashed soldiers....
* "Surface Tension" [[spoiler:shows us an Iconian. And they are ''OP as hell''. One Iconian casually kills all six members of the High Council without a second thought, then gives this line:]]
-->[[spoiler:'''Iconian:''' We give you a ''single'' warning: ''Do not attract our attention again.]]''