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Nightmare Fuel: Star Trek: Deep Space Nine
Cardassian atrocities during the Bajoran occupation. In "Duet," Kira describes the horrific conditions at the Gallitep labor camp she helped liberate.
Kira: All those Bajoran bodies, starved, brutalized. You know what Cardassian policy was? Oh, I'm not even talking about the murder. Murder was just the end of the fun for them. First came the humiliation! Mothers raped in front of their children, husbands beaten until their wives couldn't recognize them, old people buried alive because they couldn't work anymore!
The Cardassian attitude towards the Bajorans, chillingly summed up in this monologue:
Darhe'el (actually Marritza): Oh, no, no, Major, you can't dismiss me that easily. I did what had to be done. My men understood that, and that's why they loved me. I would order them to go out and kill Bajoran scum, and they'd do it! They'd murder them! They'd come back covered in blood, but they felt clean! Now why did they feel that way, Major? Because they were clean!
In The Jem'Hadar, the titular aliens attack a retreating Galaxy-class starship (the same class as the Enterprise from TNG). And the Jem'Hadar destroy it by ramming it. All to send a message to the Federation, the war goes downhill from there.
O'Brien: "We were retreating. There was no need for a suicide run."
Sisko: "They're showing us how far they're willing to go."
Illnesses and severe injuries to Changeling characters play up the body horror trope. For example, in "Broken Link," Odo has difficulty maintaining solid form due to an infection inflicted on him by the Founders. It's ... not pretty.
The morphogenic virus created by Section 31 deals a serious dose of body horror to Odo and the Female Changeling in the latter episodes of season 7. Their physical deterioration is visually disturbing.
When Garak tortures Odo using a quantum stasis device in "The Die Is Cast," Odo is unable to regenerate, and his appearance becomes horrific.
Let's not forget Mirror!Odo's messy explosion when Bashir shoots him with a phaser in "Crossover."
Lovingly called "Explodo!" by the fans.
In "Facets", Dax interacts with each of her previous hosts in the person of her friends. Most of these are cute, sweet or funny, but then we get to Joran. Not only does Avery Brooks use an incredibly creepy voice to Hannibal Lecture Jadzia, he uses the security forcefield to Inflict Electric Torture on Sisko. When Jadzia drops the field, Joran!Sisko attempts to strangle Jadzia with one hand.
Apparently, there's a take of Joran that's even creepier.
'Hard Time' brings us the Argrathi 'prison system', which uses implanted memories to compress years of horrific confinement into a matter of minutes. O'Brien gets a full two decades in a couple of hours after being charged with "espionage" (read: asking polite, innocuous technical questions), and the impact it has on him is both heartbreaking and utterly terrifying.
Another 'O'Brien must suffer' episode, 'The Assignment', brings us the very memorable first appearance of the Pah-Wraiths. One of them possesses Keiko and uses her as a hostage in an efficient and sadistic manner that's all the more unsettling for how casual it is. The sequence where the Wraith calls O'Brien about his rapidly-approaching deadline whilst combing Molly's hair is pure Adult Fear.
The Pah-Wraiths in general, in fact, are just plain creepy, as are their followers. "Covenant" throws Dukat's creepy personality into the mix to make him an all-too-believable Jim-Jones-style cult leader. What's most nightmarish of all about this cult is that they're not kidding and neither is Dukat (though he's not being straight with them about his actual motives for serving the Pah-Wraiths either). As Kira states at the end of the episode, he really does believe in his new-found religion, which just makes him all the more dangerous.
Number three for O'Brien's suffering on the page, we have Whispers. Long story short, the O'Brien narrating the episode is actually a clone, who is killed at the last minute of the episode. The terror, as pointed out by SF Debris, is that no one realizes just how perfect a clone he was. Except for the mental command to attack a senator, the clone!O'Brien is in no way different from the real one. Same memories, same emotions, and with no evil tendencies. He's just...killed. Unceremoniously. No one in the room cares that he's dying. He did absolutely nothing to deserve his fate. Dying scared, confused, and alone.
The Breen. They only appear in a handful of episodes, but they certainly make an impact. For one, their technology is different, more advanced, than anything the Alliance has, able to destroy the Defiant in five minutes. Second, we know NOTHING about them; their culture, motives, even what they look like under those suits, all are left mysterious. And finally, we don't even know what they're saying. The Universal Translator seems to translate their speech, but it's all R2-D2 Speak to the audience. All we take from them is what we see: they're Dangerously Genre Savvy, unpredictable killing machines with absolutely zero mercy. The Breen epitomizeNothing Is Scarier.
In "The Quickening", Bashir thinks he's cured a blight that has affected a planet for centuries. Needless to say, he realises he hasn't when people start screaming.
In an episode in which someone is killing Kira's resistance cellmates, they send her messages saying "That's one", etc. as each person is killed, in a deeply creepy Saw-type distorted voice. Even creepier? They use Kira's voice.
There is a dose of Body Horror when we find out who is the killer. It gets worse when we find out that he's like that because of Kira. And there's an uncomfortable dose of Fridge Horror as we find out that she regularly crippled and mutilated Cardassians incidentally as part of her resistance activities. The fact that she found all Cardassians on Bajor - including children and innocent bystanders who never picked up a phaser - legitimate targets just adds to the Nightmare Fuel. Turns out Bajorans and Cardassians aren't that different after all, and not in a good way.
In "Field of Fire", when the insane Vulcan murderer is revealed, he says he committed his crimes because it was logical.
Another creepy moment happens when Ezri and the villain, both using guns which can see through walls, find themselves aiming at each other, at the exact same time, from all the way across the freaking station.
And the reveal that the Founders weren't even directly responsible for the damage done in that episode.
That lovely scene when the Bajoran woman hangs herself on the crowded Promenade.
The Dominion has "Houdini" anti-personnel mines, which hide in subspace and make you "disappear" — at a randomly chosen instance, not by predictable rules. So basically, if you have no way to detect them, nowhere is safe anywhere they've been laid, even places you've passed hundreds of times.
There's Fridge Horror in this, too. Houdinis were poor anti-personnel devices, and absurdly bad area-denial weapons; they exist only as weapons of terror—designed to torture the Starfleet personnel with constant stress and paranoia.
What makes the most horrifying scene of all involving them so awful is that the horror is retroactive; you may just feel the need to recite an expletive when Sisko & company finally get their device working to strip away the mines' concealment, and you get to see just how many of them there were.
"Far Beyond The Stars" is just full of terrifying concepts. The denial of freedom, social ghettos, and sickening racial prejudice accompanied by dehumanization being shown as reasonable common everyday occurrences is bad enough, but Ben screaming "I'm a human being!" and ranting in despairing protest is highly disturbing in more ways than one. That it really brings home the horrifying reality of being stuck in a world where you are treated as subhuman and inferior just because of your skin color (or gender... or any other distinguishing genetic feature/s which manifests in a phenotype that contributes to appearance) is just an added bonus, of course. The accompanying Fridge Horror that even nowadays racial tensions in America are still a serious social undercurrent is just not helpful.
Dukat's obsession with Kira gets creepier and creepier. The scene in the captain's office during 'A Time To Stand,' where Dukat places his hand on Kira's cheek can easily be seen as a prelude to him attempting to rape her. Remembering that to the Bajorans, Dukat is essentially Hitler makes it unsettling, even before factoring in his relationship with her mother.
Tribunal, being another "O'Brien must suffer" episode has the scene where, after being taken prisoner by the Cardassians, O'Brien is "processed", for a crime he has supposedly committed (except no one will tell him what that crime is). He is ordered to remove his clothes and when he refuses, instead stating his name, and rank, and asserting he is a Federation citizen, he is forced against the wall by two guards who proceed to forcibly rip his clothes off him. He is then forced onto the floor where a retinal scan is taken (and from O'Brien's reaction, it's suggested the scan is painful) before he is dragged to a rather sinister-looking operating table. He briefly tries to escape but is punched in the face by a guard and restrained. Then he appears to be drugged with some sort of hypospray, while a lock of his hair is cut off and a tooth is forcibly removed, without the use of anesthetic. It's even more graphic and unpleasant to watch than what Picard went through with Gul Madred in TNG, and this is before we even get to the mockery of justice that is Cardassian jurisprudence. Earlier in the season, during The Maquis two-parter, Dukat had arrogantly boasted about the "perfection" of the Cardassian legal system (that the verdict is always decided beforehand, it's always guilty, and that "trials" are really nothing more than scripted televised farces designed to show the terrifying power of the Central Command, and also, it's implied, as a twisted form of entertainment for the public who enjoy seeing "justice triumph over evil") except now we actually get to see how terrifying this system actually is.