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Issues #1-4: The Return of Queen Chrysalis
- The entire sequence of the townsponies being replaced by changelings in the first issue. It's downright surreal seeing everypony acting inexplicably zombie-like. What makes it worse is the first ponies we see acting like this are the CMC, and at that point it hadn't been revealed that they'd been kidnapped and replaced, making it look like a couple of kids got brainwashed.
- Throughout the arc, Chrysalis is occasionally illustrated in a downright grotesque fashion.
- Almost everything the Changelings do. When they're not acting like the aliens from Invasion of the Body Snatchers, they're acting like just-this-side-of-kid-friendly Things. "Infected" indeed.
- We see the process of a pony being forced into a cocoon demonstrated on sweet little Derpy Hooves, and the mucus they use is drawn with rather disturbing visceral detail.
- Changing into Pinkie Pie of all ponies to combat the group. Think "Too Many Pinkie Pies", only all on evil mode.
- Even worse in issue #3 where Chrysalis and her minions utterly take over a village of adorable, innocent cat-like creatures filled with WUB- errr love and consume them! Remember: this is what they wanted to do to Equestria!
- Queen Chrysalis herself is a lot more frightening in the comic book version. Her looks can especially kill. Particularly, her first appearances in Issues 1 and 2 are utter Nightmare Fuel showing off her demonic side (especially as Issue 2 has her angrily glaring with her teeth bared), although the rest of her expressions tend to be more comical. As of Issue 4, it's even implied that she's willing to consume the CMC regardless and things get a lot more scary as the story goes on. Even the covers featuring her of issue #4 is more frightening. And all of that drool and vampire teeth too!.
- In issue #3, Chrysalis takes one of the left over kittens and in the next panel, all you can see is a white background splattered by black and the Cutie Mark Crusaders' screams, the implication being that she mauled it to death in front of them.
- The cover of issue #3, featuring the Mane Six minus Twilight as Changelings. Also the cover of issue #4, with the Mane Six trapped in Changeling goo as a giant Chrysalis in the background bares her fangs.
Issues #5-8: The New Nightmare Moon
- Given that the entire arc is about nightmares, this was inevitable.
- The entire premise of the arc is rather freaky when you put yourself in the ponies' position. Imagine being plagued for a week with nightmares, unable to get a good night's sleep. Desperate to fight them off, they have a sleepover, reasoning that if they're together, they won't be scared. They still have nightmares (and very realistic ones, at that). The ponies then awake to find Rarity screaming and being dragged out of her bed by an indistinct black mass. They're unable to save her. The entire concept is something straight out of A Nightmare on Elm Street.
- When they're having the sleepover, Rainbow Dash has a nightmare about watching other pegasi flying while she can't. Why can't she fly, you ask? Because her wings have apparently been shredded almost completely off, leaving a pair of thin protrusions that appear to be the front edge of her wings, with the rest of them nowhere to be found.
- And remember, flying is Rainbow Dash's WHOLE LIFE. Imagine how she would feel if that really happened.
- Some of the other nightmares are also pretty unsettling. Highlights include Celestia dismissing Twilight from her studies forever (similar to her dark magic-induced nightmare in the season 3 premiere), Applejack's whole family surrounding her with pure hatred in their eyes after all the trees on her farm died (a wrathful Granny Smith is really something to behold), and Fluttershy's animals running from her like she was the plague - including a few bunnies, one of which may be Angel.
- NIGHTMARE RARITY. Especially after it's revealed she can control dreams and nightmares.
- The whole arc has some really dark imagery. When Nightmare Rarity is trying to persuade Spike to join her, she gives him a scepter and tries to place a crown upon his head. When he snaps out of the dream, it turns out the "scepter" is actually a broken stick. The "crown" is even more unsettling: it's a really creepy-looking mess covered in dust and cobwebs with a chain hanging off its side, emblematic of what Nightmare Moon II was about to do to Spike.
Issues #17-20: Reflections
- Celestia disappears one day, with even her sister uncertain of what happened to her after seeing her vanish through a magic mirror. At the end of the first issue in the arc, Celestia re-emerges from the mirror, battered and bruised, ultimately collapsing into her horrified sister's embrace... and the shadowy figure of King Sombra is shown in the mirror's reflection...!
- Worse? It wasn't Sombra's fault, that Sombra is a good guy. It was actually done by Mirror!Celestia and Luna.
- The reactions of the heroes (and audience) upon seeing Mirror!Canterlot... The castle town is in ruins and a dull volcanic gray. The sky is a crimson red with dead trees and several broken statuesnote . The major contrast with the colorful and beautiful normal Canterlot is just jarring...
- When Twilight notes how bleak everything looks, Rarity makes the comment that seems to be on everyone's mind: is this what their Equestria will look like if they fail? Considering everything from Nightmare Moon and Discord to Chrysalis and Sombra, it really cements just how much is at stake each time a new evil rises.
- Taken to a whole new level when back in the Season 4 finale, Tirek absorbs everyone's magic except the princesses'. When Twilight goes to face him, the sky is the same sort of red as Mirror-Equestria, showing just how close the nation was bought to the same level of ruin.
- Up to Eleven with the Season 5 finale. With Starlight undoing the Sonic Rainboom, we see several bad futures of villains winning. From the eternal night of Nightmare Moon to the ruins by Tirek, or even the horrific unexplainable wasteland near the end, it is truly frightening just how much is at stake each time our beloved protagonists fight.
- The obviously fake smile on Mirror!Celestia's face as she "affectionately" strokes her sister's chin... while already planning to backstab her. Worse, Mirror!Luna takes this gesture at face value, even though Mirror!Celestia has never been particularly trustworthy to begin with.
- AU!Sombra's FaceĖHeel Turn is brought about by an obviously very painful transformation thanks to the Elements of Harmony.
Issue # 23
- Everyone in Ponyville is being mind controlled by the villain of the story and now they are tearing apart a dam to flood their own town. Worst of all, the Mane Six are among them. Itís pretty disturbing to see the heroines who usually save the day as mindless thralls, especially since one of them is an Alicorn princess.
- Especially since we never get to know exactly why it was necessary to hypnotize the ponies. Since the issue with the pirate captain, it is established that the Kelpies are friends of the ponies, so it has no meaning to hypnotize the ponies of Ponyville, even if it means to carry some water sprites back to sea and a dam lies in the way.
Issue # 24
- The Bad Future that Discord & co. end up visiting by mistake.
Issue # 25
- Our look into Angel's head in the short "To Tame the Beast." The gorgeous artwork really lets it look horrifying.
Issue # 33
- The Adult Fear introduced when the CMC are left alone with Flutterbat. They are three CHILDREN, watching a monster.
Issue #34-37: Siege of the Crystal Empire
- Radiant Hope Jumping Off the Slippery Slope with her plan to bring King Sombra back. A dark Deconstruction of The Power of Friendship if ever there was one.
- And speaking of Sombra, his Living Shadow Nightmare Face just before Hope revives him practically screams The Power of Hate.
- Sombra turning Celestia and Luna to stone with minimal effort, abruptly subverting their Big Damn Heroes Hope Spot and effectively putting them on the receiving end of the way they defeated Discord.
- The Reveal of the Umbrum's true identities — not the pixie-like beings that Hope has grown accustomed to over the centuries, but Shinigami-like Eldritch Abominations that wouldn't look out-of-place in something like Attack on Titan or Bleach.
- Not only that, but the sheer Mood Whiplash as soon as Cadance uses her magic and inadvertently reveals them. Up until then, they're nothing but friendly (or even Affably Evil, provided that you shared Chrysalis's suspicions all along).
- Furthermore, the fact that Hope lived with these things for over a millennium. Imagine your best friends, neighbors, etc. turning out to be Evil All Along and cruelly shattering your entire worldview in an instant.
Issues #38-39: Don't You Forget About Us
- The CMC, Diamond, Silver, Snips, and Snails being chased by a wild BEAR. Especially when its sniffing around right above their hiding space. The fact the foals are scared to death with Apple Bloom and Diamond Tiara clinging to each other just makes it more terrifying.
- To close out Issue #38, Diamond Tiara slips off a cliff and clings onto a root to keep herself from falling. Her scream and the perspective of the ground below amplifies the fear. To make matters worse, Apple Bloom falls as well and has to hold onto Diamond Tiara's tail.
- In Issue #39, after Diamond Tiara and Apple Bloom are saved, the foals become trapped by a thunderstorm which starts washing away the ledge where they are standing.
- The foals find a cave near the top of a mountain and spend the night there together. Before they turn in, Diamond Tiara and Silver Spoon become fed up with the rest of the group and consider looking for another place to sleep. They change their minds when they hear a wolf howling outside.
- It must have been a terrible night for all missing foals' parents and guardians, Cheerilee included. However, Rarity deserves special mention. She's seen rushing to Sweetie Belle before anypony else, her mascara smeared and her hair messy — a jarring contrast to her usual cleanness and elegance. Poor girl must have been crying all night over unintentionally providing the distraction that helped her little sister (and six other kids) get lost.
Issues #43-45: Ponies of Dark Water
- The very hot spring that corrupts the Mane 6. You could just be stumbling along it one day and decide, "hey, I could totally take a dip in this", and then wake up the next morning doing horrible things to those around you. In fact, that's exactly what happens! Oh, and it makes you able to resist the powers of a Physical God! Seriously, imagine how much of a threat Applejack would be if she didn't Know When to Fold 'Em.
- Even worse, it's implied that the Mane 6 were fully aware and in absolutely no control of their actions. As soon as they come to, they immediately regret their actions and remember everything they did. Bonus points for Rarity, who already suffered this kind of fate less than 40 issues ago, and Luna, who has to deal with becoming Nightmare Moon, an event so traumatic for her that she felt the need to psychologically torture herself, again.
- Heck, the entire concept of the Mane 6 suddenly turning evil makes for some great Paranoia Fuel, especially if one or more is your favorite character.
- Corrupted Pinkie Pie is basically The Joker; funny, but purely psychotic to the core...
- She also creates water balloons filled with the tainted water, which can turn anypony hit with it evil a lot faster than the spring in its natural state, resulting in the rebirth of Nightmare Moon, if only for a little while.
- On that subject, Nightmare Moon does quite a number on Pinkie Pie. Any more, and there wouldn't even be a party after the threat is taken care of...
- Corrupted Rarity is essentially a fashion-obsessed Doctor Doom, mask and all!
- Corrupted Fluttershy, basically the pony equivalent of Poison Ivy, shows just what could happen if the talent of taking care of animals was taken full advantage of; she even sics them on the Cutie Mark Crusaders! And by the time of the final issue of the arc, the animals are about to go to war.
- It's also a possibility that Fluttershy's corruption spread to some of the animals themselves, and they were also fully aware of what they were doing.
- Corrupted Twilight Sparkle gets it the worst, so much so that the Crusaders and Spike declare her the most immediate threat. She declares herself Empress of Ponyville, is obsessed with intelligence to the point where she drains it out of other ponies (except Bulk Biceps), is more than capable of overpowering Rarity and Luna, and is Crazy-Prepared to the T! Many fanfics declared that a face-turned Twilight Sparkle would be one of the worst threats Equestria would know, and this comic proves them all right; the only thing that did her in was her own lack of a sense of humor.
- Combining the Pinkie Pie entry with this one, if Nightmare Moon actually offed Pinkie Pie, the chain of events that leads to the other ponies getting cured wouldn't have happened. Even if it somehow did, Twilight would be impervious to any and all other plans. If there was no more Pinkie Pie, nothing would stand in her way.
- Retroactive one. Many questioned why Celestia didn't get involved personally. Once we see her evil alter-ego unleashed, there is no more question.
- Finally, Luna outright says they only defeated the corrupted Mane 6 because it made them too self-interested to work together, but that they'd be unstoppable otherwise... The end.
Issues #48-50: Chaos Theory
- "Imagine. Imagine. Imagine. Imagine."
- Accord projecting his face onto his brainwashed victims and speaking through them makes for a deeply disturbing effect.
- The fact that, not only did the elements of Harmony not work on Accord, they worked in his favor and made him spread his mind control even further! He even got the rest of the mane six, Spike and Princess Celestia! If it wasn't for Starlight, he would've succeeded in his plan.