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- Starlight's anxiety attack, the camera zooming in on her face as her face fills with terror and anguish. Twilight's voice fades into the distance. Starlight clenches her eyes shut as she's sweating profusely and a pervasive white noise rings. Some have noted that this is a disturbingly realistic portrayal of Post-Traumatic Stress Disorder.
- The Grim Up North Crystal Empire has weather so powerful that not even a pair of alicorns working together can delay a blizzard for more than a couple hours. That is scary enough by itself but for Equestrian ponies it is doubtlessly much worse since they are used to having the weather under their control.
On Your Marks
- Apple Bloom setting up a Room Full of Crazy after she tries a lot of things on her own, but can't enjoy them. When Sweetie Belle and Scootaloo find her, Apple Bloom is sitting on her own, in the dark, staring at her failures. It's actually fairly creepy to hear the normally jovial filly talking in a Creepy Monotone with her Face Framed in Shadow.
Oh, hello girls.
Have fun pursuing your own
Gauntlet of Fire
- There's something very unsettling about watching the armored dragon (Princess Ember) sinking down into the sea, dragged under by the weight of her armor. The overhead shot of her slowly disappearing doesn't help at all.
No Second Prances
- Trixie still being willing to go through with the Manticore Moonshot Mouthdive without Starlight. After admitting that she couldn't do it on her own, and Trixie openly upset about ruining things with Starlight, the implications of it are unsettling.
- The scenes where Hoofdini and Trixie perform the Manticore Moonshot Mouthdive. Even though both of them end up just fine after all is said and done, the trick itself is absolutely terrifying to watch; the performer shoots himself or herself from a cannon into a manticore's wide open mouth, and the manticore swallows them whole.
A Hearth's Warming Tail
- As can be expected of Yet Another Christmas Carol, Princess Luna as the Spirit of Hearth's Warming Yet-To-Come is rather intimidating, showing Snowfall Frost a Bad Future in which eliminating Hearth's Warming Eve leads to the Windigos coming back and blanketing Equestria in an endless winter. Made all the more terrifying by Luna's haunting song and the fact that aside from the Windigos there is no trace of life anywhere in the Bad Future.
- Luna's entrance also qualifies.
28 Pranks Later
- The "cookie zombie apocalypse".
Every Little Thing She Does
- Starlight Glimmer, in hopes of getting everything done fast and without a hassle, casts a spell that makes all of the Mane 6 (sans Twilight, who left earlier) obey her commands. Aside from the ponies being incapable of their own free will, there's also outward features such as shrunken irises, an emotionless tone of voice and an odd, robot-like behavior that comes off as unnatural and disconcerting (not to mention the way they felt after the spell was undone). One moment that stands out in particular is mind-controlled Fluttershy covered in insects and snakes◊ and acting like nothing is wrong.
- While it's a Shout-Out to Predator, Applejack mentions in passing that Big Macintosh had to cover himself with mud to hide from a "creature." Exactly what was so big it could scare Big Mac?
To Where and Back Again
- In-universe example: Starlight's return to Our Town, and her confrontation with her past. The ponies of Our Town repeatedly asking Starlight for advice and guidance is uncomfortably similar to a recovering alcoholic repeatedly being offered drinks. The poor thing looks terrified. She later says that she never wants to be in charge of anything ever again just like how one might fear a single drink knocking them off the wagon.
- Before that, Starlight has a nightmare when the villagers rip their invitation in her face and laugh at her... all while taking the very same, creepy, hollow smiles that she used to force onto them.
- The Dwindling Party is treated with uncommon seriousness. Trixie running away from the Changelings ends with a Dog Pile of Doom and Fade to Black that sure looked final. Discord's final scene on the other hand somehow makes Fluttershy terrifying, and features one of the few moments when Discord looks truly vulnerable.
- In this episode, Queen Chrysalis and the Changelings prove to be much more frightening than when they invaded Canterlot.
- The Changelings are very aggressive and numerous, not to mention smart as well. Although Discord and the others both saw through the enemy Changelings' disguises, they still managed to get half of the party captured that way (Discord because he was lured and Trixie because of the aforementioned Heroic Sacrifice).
- Queen Chrysalis' entrance when Starlight (who is actually Thorax in disguise) enters the throne room. Not only does she move like a spider, emerging from behind the cocoons containing Princesses Celestia, Luna, and Cadance, she moves like she has no bones at all (and that includes her head), complete with twisting sounds.
- Hell, Queen Chrysalis in general. For example, she tosses Starlight around like a rag doll (and she couldn't even fight back because of non-Changeling magic being nullified) and mercilessly holds Thorax up in the air as she drains him of his love.
- We also see up close just how horrifying it is to be trapped in a cocoon, which doubles as a Tear Jerker. Not only are the victims completely helpless, unable to move beyond a jerk of the hoof, but it's implied that, despite the serene feeling they're in, the victims suffer psychological torture as they're trapped, begging to get out.