Rarity's first chapter. The other girls get a Journey to the Center of the Mind, or some sort of fantastic element. Rarity gets plain, vanilla PTSD — and you get to experience her fear in first-person!
There is this one nightmare she ends up having that is particularly disturbing; Tom crashes into the boutique, bellowing for Rarity to marry him. Rarity begs him to stay away from her but suddenly a cockatrice pops out of one of the bouquets he's holding and turns her to stone. Rarity then stands there, terrified, helpless and immobile as a bunch of rock servants show up and force her into a wedding dress. Tom then excitedly declares that he and his "rock princess" will be together forever…whether she wants it or not. Not only is it scary, but it's also practically dripping with Marital Rape License implications.
Worse? The latest dive into the Bad Future reveals Greedity views "Tom" as her husband and her rocks as her babies.
The Audio Adaptation makes all of this absolutely terrifying. Especially when Rarity snaps and goes berserk. The voice actor's emotion really helps.
Loneliness. Everything about her and everything she does is absolutely terrifying.
The Bad Future where Discord is the absolute master of the world. Let's just say that the dead rising from their graves to devour the living daily and the fact that he has magic users, even fillies mass executed are the least horrifying things his reign entails.
Discord basically turned the Mane Six into his version of the Nazgûl, and is shown forcing all of them, but especially Twilight Sparkle and Rainbow Dash, to relive the moment of their utter damnation over and over again.
As surprising as it sounds, the audio adaptation is worse. The images, which pull no punches don't help one bit.
Also, somehow, the audio adaptation manages to make sleep-deprived Pinkie sound TERRIFYING.
Applejack's reharmonization shows what happened to the ponies of Equestria when Discord took over and their PSTD afterward; some of it (like Dr. Whooves calling himself "Queen of Eagleland" and Photo Finish streaking and eating her own dresses) are hilarious, but most aren't, like Apple Bloom being turned into a necropony, Diamond Tiara and Sweetie Belle being turned into dolls, Bon Bon being turned into her namesake as her best friend Lyra squeezes and tries to eat her, Derpy wishing death on her daughter, Dinky, Silver Spoon's father trying to kill her with an axe, Twist's limbs twisting wildly out of control, Prince Blueblood being turned into a living ice sculpture of a mare being chased around by a living sun that wants to rape her to death and Philomena being forced to rebirth herself repeatedly and then being reduced to ashes, placed in an urn and tossed into the deepest of the Gala's fountains. The following sums the whole sequence up perfectly;
And AJ knew, AJ KNEW, that this was only a TINY PORTION of every pony in Ponyville!
Not to mention the visuals in the audio adaptation showing what the other ponies went through, each bit actually narrated by said character. What happened to Lyra and Bon Bon really sticks out in this troper's mind... shudder...
The part near the end when, in an effort to stop herself from closing the Well, Applejack jams her hoof into the gears.
It says a lot with the Nightmare Fuel and depravity of Discord's in other fanfics has begun to be measured using this story's Discord as a ruler.
It also makes the aboved mentioned Wham Line even more terrifying. Not only is the line monstrously distorted, we get a lovely picture of Loneliness's equally monstrous eyes.
Rainbow slowly turning into…something in her "True Healing" chapter. Fluttershy and Pinkie stopped it in time, but still…
As can be expected, the Audio Adaptation makes this about a thousand times worse. Not only are the visuals are terrifying, the distortions of her voice makes it absolutely terrifying.
Fluttershy's transformation into a Nightmare Moon-esque monster, and Fluttercruel possibly dying immediately after. Even the author admits he went too far with this one.
Princess Gaia brainwashing the reader at the beginning of "Teacher Teacher". Made even worse by the fact she still acts like Fluttershy, which makes it much creepier.
We finally get a good look at the Ponyville Bedlam House Screwball stays at…just in time to see Princess Gaia Mind Rape most of them out of frustration. And then there's the Pegasus who seems to regain her sanity, only to realize her wings have been chewed off.
Princess Gaia changing "Everfree" to "Everkind". It's like she's taking away their freedom, forcing them to live in her own world, whether they want it or not.
Luna outright exploding at Fluttershy and Fluttercruel for their crimes. Its pretty much Mind Rape.
And the published version was edited, the original was apparently a good bit worse!
Celestia making a full 180 after an entire chapter of "good cop" and doing just about the exact same thing Luna did (only goes more out of her way to comfort Fluttershy after the What the Hell, Hero? part is over with), but this time without giving 'Shy the comfort of her alter ego. It was enough to make her stain the mental floorboards.
Nightmare Granfalloon deserves special mention for being completely Ax-Crazy and scary as all get out. Some readers even admit that she gave them nightmares. now in fanart form.]]
Nightmare Granfalloon: Anger is dead-dead-dead! Pinkamena is dead-dead-dead! Bad foalhood memories are dead-dead-dead! Now there's only happy thoughts!
A bit of Fridge Horror about that? Remember that Pinkie's foalhood memories are represented by a baby version of herself…
It's not as obvious as the Brave New World universe, but it's certainly pretty dark. Even with Princess Gaia leaving a lot more free will in the process — Applejack's suggestion that Gaia didn't take in the central POV universe — it's still very much an assault on agency and personality. May count as an Esoteric Happy Ending for others, though, depending on how much you count being foaled as Mind Rape, as it isshrinking the sum of all evils in Equestria.
When he was Discorded, Silver Tongue tried to kill his daughter Silver Spoon with an ax. Let's just say the Emergency Response Team was very fast.
The effects of Onyx Tiara being Discorded: everypony he touched (save for himself — and yes, he tried) became a physical match for his beloved wife, whom he'd lost to mental instability. He proceeds to turn all of his servants into a harem of false Golden Tiaras, consummates with them — and when his real wife shows up, mind cleared and willing to love him despite finding him surrounded by his clones? He dismisses her as a parody and drives her off in tears. As if we needed any more proof Discord is a Complete Monster…
And then when the Mane Six defeat Discord he awakens to find himself surrounded by his traumatized servants, one of them a horrified colt, and they all remember everything that happened. EVERYTHING.
Oh, and the colt? Let's just say there's a reason Featherweight didn't talk in "Ponyville Confidential"…
Entropy. Just Entropy! The entire scene with her is just terrifying.
And if a certain Loose Canon story is to be believed, she can literally make it so you never even existed to begin with.
We see later in origin Discord's reign in all its horrifying glory, but one that stands out is his previously mentioned Flutterpony genocide. He made a public butterfly collection out of them.
Galaxy/Wind Whistle's (Celestia refuses to tell which) fate. Dear lord…
Made worse by the fact he morphs her body into his. And just imagine how Twilight feels hearing that the Discord she and her friends encountered was a spirit using a pony's body as a host!
Discord's treatment of Diamond Tiara. He alternates between abusing her verbally and just flat (mundane) out Mind Rape, stringing her along with enough praise to keep her listening to him. What makes this even more terrifying is this is how actual abusers behave!
And how can we forget the utterly charming dream dear Diamond Tiara has while sleeping in a Canterlot park? The one where she finds herself alongside thousands of other ponies — Earth Ponies, Unicorns, Pegasi, Flutterponies, even sea ponies — pulling a massive chariot with a gigantic horned serpent in it whipping them all and laughing as he roars, "Cry Havoc!". Word of God is that the scene was based on a similar one from All Dogs Go to Heaven.
While Diamond Tiara is in Canterlot she runs into a rather…disturbing Stallion. Who tries to kidnap her and do Celestia knows what to her! The only thing we get about his plans is this:
Stallion: You'll make such a wonderful doll. Pretty, silent, and obedient. Don't worry. You'll be pretty forever. I'll wipe away all those painful and annoying memories. They'll be nothing except being a nice little doll for ponies to look at and play with.
In a later chapter we find out that Filthy Rich's unicorn maid apparently met that same green unicorn. He did… things… to her that left her with a phobia of the color green. She was handling it, but unexpectedly seeing something green could set her panic attacks off. Then come the Day of Discord and guess what Discord made everything look like to her. Though it could have been worse. She could have turned everyone she touched into him, like Filthy/Onyx and his wife.
Although things thankfully end well, in the Loose Canon story "Not One of his Kind", seeing Canon!Discord's version of Fluttercruel trapped in Limbo, covered in bloody scares and missing both her wings and almost all of her limbs was pretty unsettling.
The trailer for the audio version of "Reharmonized" manages to take the hilarious "Queen of Eagleland" speech and make it utterly terrifying.
In keeping with the tone of "Discorded', the trailer focuses on the darker parts of "Reharmonized", including, among other things, Loneliness' reveal, Angry Pie's rampage, Mitta being dragged back to Sunnyville at the end of the Gaia arc, Silver Ax's rant, and, of course, Discord.
Also during the Mind Games arc, we get another glimpse of the Epilogue timeline (or a similar enough one) via a nightmare shared by Rainbow Dash and Scootaloo. In it, Traitor Dash kills an adult Scootaloo (who's apparently a Rebel Leader), and Discord decides to "reward" her by creating a play about her victory, and having her attend every single performance. Oh, and a detail that shouldn't be overlooked — during the fight, Scootaloo runs Traitor Dash through, but she doesn't die because the Element of Chaos Discord gave her has taken the place of her heart.
Worse? We later find out how that happened. He literally shoved them into their chests.
"Different From Everypony Else" gives us a depiction of Discord's attack on the insane asylum outside of Ponyville. What he did to the ponies working there, who, despite Onyx's opinion and how Discord depicted the place, are pretty decent ponies, is just absolutely horrifying. And the scene ends with Discord holding down the character whose point of view we're seeing through and preparing to drill into his skull or something equally as horrifying we thankfully don't see (he didn't kill or seriously hurt the guy, but that doesn't change what happened!).
Discord: This will only hurt for a second! So be sure to struggle and squirm a whole lot!
Mind Games Part 8. Discord finally manages to break Diamond Tiara, and she breaks so hard that she goes Nightmare. She even gets a new Cutie Mark out of it: the Star of Chaos.
The sight of the Sea Ponies in the Epilogue Timeline. Sure, it seems nice on the surface, then you solely realize they know only a history their version of Discord wrote, completely unaware the original ones were wiped out by him and he uses threats of their destruction as part of a Sadistic Choice with Traitor Dash without a second thought.
Want to know what's worse? One of the snide nicknames Six had for the Valeyard in Trial of a Time Lord was "Knacker's Yard".
A mysterious voice has started answering readers' comments since the Dark World Arc started. We don't know who or WHAT it is, except it doesn't seem to be Discord (and seems to hate him) and is very creepy in rather subtle ways.
The voice isn't confined to the comments anymore; something is talking to Twilight Tragedy, goading her on in certain directions. It's very creepy. We ultimately learn that it's Sparkle, a third part of her personality that utterly hates Discord and her once-friends and wants to destroy Equestria and kill everypony to end her pain…or so it seemed, as the statements continued after she faded away…
During the audio adaptation of Rainbow Dash's reharmonization story, we see an image of a terrified Scootaloo running in fear from her Discorded friends, that is…unsettling to say the least.
Fluttershy's fate in the Epilogue Timeline. Queen Cadence tells the Elements in her final battle that Fluttershy is still alive inside Fluttercruel and is so horribly broken by all the horrible actions her body has done that she just wants to die to stop Fluttercruel.
The final fate of Cadence. That sound you hear is your brain trying and failing to delete the image of Fluttercruel devouring Cadence out of your memory. Have fun with that.
And if Fluttershy is still inside her, this means that she feels and tastes everything.
The scene in "Apple Tree" where Liarjack is dragged off by Entropy's shadows of existence, while Apple Bloom and the Father of Alicorns can only watch. It doesn't last long, but it's disturbing while it does.
A minor but downright chilling one in part two of Chapter 9 in the Dark World arc. Tom finds himself on the edge of Entropy's realm, and the pony shadow that comes for him has the same Cutie Mark as poor Toola-Roola. And Word of God definitely says that is her.
The dog/wolf…thing that's stalking Shining Armor throughout his arc. What makes it worse is that it's apparently able to Retgone anything it touches, and seems determined to do so to Shining.
Worse? In the previous chapter, he heard something sniffing around in the embassy, it was in the building with him!
After the Duel of Tears, Rarity is overwhelmed by her Element of Desire and attempts to take Rainbow Dash's Element of Treachery by cutting it out of her, knowing full well that this would kill her. Fortunately, Twilight talks her down.
The Valeyard remembering his granddaughter. Particularly nasty considering caring for his daughter is the one redeeming quality that Discord has.
The Valeyard: Ah, Susan…Haven't seen you since my fifth regeneration. Looking back from where I now stand, I so dearly miss how ridiculously easy it was to make you scream, cry, and suffer nervous breakdowns!
The Valeyard No Sellingthe Memory Spell. Not only does he confirm afterwards that it didn't work because he's not Discorded and did all the heinous acts he committed without Discord's taint, a contingency he put in place in case Twilight used it on him tries to hijack her mind and turn her into a Valeyard clone, only being stopped by having Derpy and Rarity smash her head so she could regenerate a new brain cleansed of it.
Similarly, "Love/Hate Bedlam" confirms that Fluttercruel, like her main POV counterpart, is indeed a separate being from Fluttershy, and reveals that she tortured Fluttershy for five hundred years before Cadence's spirit saved her, and is only upset that she can't do it anymore. The Elements of Harmony are horrified and disgusted by this, and Rarity actually goes into a Tranquil Fury over it, saying that she'll kill Cruel for it.
In Dark World Part 20, it's revealed that Fluttercruel inherited Fluttershy's Stare and intentionally held it back as a trump card in case the others went rogue. She was capable of using that power all along and nearly killed Rarity with it. The only thing that saved Rarity from getting butchered was some pragmatic use of Tom's fragment.
Angry Pie brutally takes down Twilight, smashes her horn, and even steals her Element. The chapter ends with Twilight slowly drifting out of consciousness.
In the following chapter, Twilight turns out to be Not Quite Dead... and she proceeds to start torturing Angry Pie to death, saying how she's tired of trying to reason with Angry and is going to "end her". Aside from the obvious He Who Fights Monsters aspect of this, there's the even more horrifying implication that she's turning into a Nightmare in the process.
Possibly just as frightening, the Voice's reaction to this. 100% supporting Twilight going Knight Templar.
The mental Hell Twilight sticks Angry in, complete with a monster version of her (probably her Nightmare self) tormenting her. Fortunately, this gets called off before it goes too far, but still...
The group's reactions to Rancor/Disruption opening a portal to Entropy's domain. They are all absolutely terrified by a mere glimpse of Entropy; this is the first time we've seen a normal pony's reaction to viewing an Eldritch Abomination, and it's as bad as you'd think.
Seeing Rancor consume the shadows of existence is creepy to say the least, but at least she was made to become one of them. To think that you're watching a pony eat those same shadows is very unsettling, especially in that her teeth changed by eating before the rest of her body changed.
Fluttercruel's MEGA Stare. It comes from everywhere! And works uber powerfully.
Shady's spirit appears in Dark World and says the Nameless Passenger is worse than Discord. She outright admits that Discord's been a monster (even if she still loves her son), but still considers the Passenger worse. Let that sink in for a moment.
Discord's death. Entropy drags him into her realm through his chest wound, pretty much making him implode.
The Reveal in "All Things In Twilight". It turns out the entire Dark World arc has been a "Groundhog Day" Loop created by the Nameless Passenger to eternally torture Discord, and its been going on for eons. When the Passenger is trying to convince Twilight to reset time to before the events of "Return of Harmony" (which, by the way, would result in the deaths of the several million inhabitants of the Dark World, many of which are completely innocent), we're shown several of the time loop's past conclusions in rapid succession, each one more terrifying then the last.
The worst part? The Passenger's true identity; Twilight'spotentialNightmare. And she manifests herself by possessing Wind Whistler's rotting corpse.
Gets even worse in "Give A Reason" as we get to know Nightmare Eclipse/Paradox. Between her actions, her Faux Affably Evil personality, and just how much she's like Twilight, she is absolutely frightening.
There's also the Simurghs, eagle/wolf hybrid mutations created by the blast (by Discord's influence) that attack in packs. They nearly kill the family if not for Scout. They actually did kill Cream, which has an added level of horror due to the fact she was fully aware of what was about to happen to her, but unable to do anything about it, not even scream. And that's if they decided to kill her and just didn't eat her alive.
Finally, the Whispering Plague, a supercharged, mutated version of The Black Death that not only kills rapidly with the normal horrific symptoms, but adds in terrifying voices actively trying to drive the victim over the Despair Event Horizon. Thankfully, Sweetheart (posthumously) and family wipe it out.
"All My Friends Are Here": The Final Battle with Nightmare Paradox contains quite a bit. One moment that stands out is her lighting Apple Pie on fire and nearly killing her!
D___t's Shadow of Existence trying to consume Bright Eyes' soul and concept. The mere idea is horrifying, though it turns into a Crowning Moment of Awesome as she fights against and ultimately defeats him.
The assassination attempt on Fluttershy. The implications that not only are a lot of ponies still enraged over the Princess Gaia incident, but are more than willing to act out their rage, is not only chilling, but casts Fluttershy's future into uncertainty. Who can you trust in a world where nearly everyone wants you dead because you made one mistake?
Clover's story has Clover, Dandy, and their son be fused together by the spell, creating G3 Minty.
Her Nightmare section begins with Clover and company emerging from the subway into a post apocalyptic Manehatten with ponies laying dead in the streets and buildings leveled. Out of all the Gaiden stories, this is the only one to show the effect on a major population center, and it is horrifying.
There's something rather unsettling about Fluttercruel's Punishment outside the normal discussions on mercy, justice and parental punishment. The biggest one would be seeing the line of ponies that Fluttercruel killed in her lifetime. It was described as "really long", but given what twilight mentioned about her, it's quite likely that the line was in the thousands at least, if not in the millions.
Shining Armor Part 14-3; the Stalker shows up again, chasing Shining across an airship in the dead of night. The real frightening bit? It's a ship that Cadance is sleeping on, and the Stalker is supposed to be incapable of getting within a certain radius of her. It's evolving, or just so determined to erase Shining from existence that it's now willing to defy a goddess to do so.
Cadance's original self, Cadenza. Seeing one of the most innocent, kindest and motherly characters in the series as a hateful, spiteful monster willing to tear her own wings off just so she could murder an innocent mare in cold blood is absolutely chilling.
Scarier? She thinks she's doing the right thing. She's seen the evil that magic can do. From her perspective, just by existing, Amicitia is the bad guy. In a way, that makes her scarier because you know in her heart she thinks she's right.
Shining Armor 15-1. The Hooviets launch a helicopter attack on a completely innocent village and some of the villagers actually die. The ponies are rightfully horrified by the brutality.
In part 2, we find out that Marakov has forcibly converted hapless ponies into killer cyborgs and has turned others into monsters! This troper can't be the only one eagerly awaiting to see this sick bastard get his just desserts...
In 17, Makarov unleashes his endgame. This involves using Deadly Gas to perform a dragon genocide, starting a global war, and finally unleashing one of his superweapons, Skyfall. What does this do? Rob everything but his flag ship and helicopters of their ability to fly, resulting in every airship, pegasi, and griffin falling right out of the sky. To make it worse, Shining hears them bouncing off the roof of Makarov's ship and knows every hit is someone dying. In one chapter Makarov manages to go from a silly Parody Sue to a mass murderer.
While also satisfying given the above, Shining snapping and trying to outright murder Makarov is rather frightening given how dedicated he is to his Thou Shall Not Kill philosophy.