Team Xen's attack on the S.S. Oceana at the start of the game. While quite similar on paper to Team Meteor's attack on the train station at the start of Pokémon Reborn, it's arguably more effective here due to the tonal shift: One minute you're listening to the old ship's captain rambling on and people making jokes and references, and the next minute the ship's been attacked with a bomb and taken over by tentacles and Deoxys clones, with Scenery Gorn aplenty.
Madelis' plan for Carotos Mountain and Sheridan Village: Using a Dimensional Rift to painfully transform a Volcanion into a generator that converts water to magma, Madelis slowly melts down the mountain, turning it into a volcano. She then plans to unleash all the magma within the mountain onto Sheridan Village, killing everyone. She even admits that this process is unnecessarily cruel, but she decided to go through with it anyway just so she could see Keta and Volcanion suffer as much as possible.
Angie's Villainous Breakdown. Unlike any other villain in the canonical Pokémon games, after her defeat in a Pokémon battle, she attempts to murder Venam, Melia, and the protagonist. The fact that even utter bastards like Ghetsis haven't tried to do this before makes this even more jarring.
A bit of Fridge Horror about Angie: She has a Dimensional Rift that she uses to suck you into her world. As far as we know, only Zetta can create Dimensional Rifts. Since Angie isn't part of Team Xen, where did Angie get a Dimensional Rift from?
The Reveal in the Stinger of Chapter 8 that Crescent was evil all along. This lady can kidnap people with impunity and banish them to an alternate dimension and brainwash people into doing her bidding. She's implied to be playing everybody to achieve her goals. If what Geara and Angie did was any indication, then it's pretty likely that simply defeating her in a Pokémon battle isn't going to do much. Thankfully, it turns out later that she's not actually evil, and things are far more complicated than they seem, but still, it can be pretty offputting to new players.
The Stinger of Chapter 9 has a close-up of Angie's terrifying face flash across the screen, corrupting the already weird place. It doesn't help that it may randomly pop up on the title screen.
Darchlight Manor. Remember Old Chateau from Pokémon Diamond and Pearl? Imagine that, but worse. If the creepy ambience and music of the area doesn't manage to creep you out, then the diary entries you find scattered around certainly will. It doesn't help that through the entire sidequest you get to interact with both the ghost of the girl who died and the possessed doll, which is heavily implied to be a Rotom. And at the very end of the sidequest? You manage to make your way to the back of the manor, where you find the well in which the girl fell to her death, and if you pull the rope you'll find the Clefairy doll, which is described to be watching you.
While the "The Hidden Library 3" Sidequest is mostly funny, there is one disturbing bit in versions before 13.5: right before you enter the Unown Dimension, A GIANT UNOWN EYEBALL OPENS UP ON THE FLOOR.
Goldenleaf Town (well, before Chapter 15- as of Chapter 15, it's been toned down a lot). You're told before you go there that the villagers don't like outsiders; while technically true, it's a massive understatement. For example, the moment you walk in, you have to prevent a lynching- and the person getting lynched is a pre-teen. The town itself is very rundown, and most of the people- including the ones outside the town gate- don't even want to battle you, they just tell you that you're a piece of shit for existing. Some of the people who do talk to you are even creepier, like the kid who implies that the villagers destroyed the Poké Mart, or the girl who implies that she killed an outsider for asking her out. Thank goodness for the Pangoro.
The aptly named Nightmare City. It's a Pocket Dimension where every single person that has a nightmare in Grand Dream City travels to instead of having said nightmare, and while they're in there they're basically reduced to a mumbling mess that can only talk about whatever nightmare brought them there. Imagine simply going to sleep one night and waking up in a hellish version of your hometown where all you can do is stand still and ramble about your nightmares until you are forced to wake up. The worse part? If you actually take the time to explore this place you'll eventually find Crescent in that very same state, mumbling about how "There's not much time left, there's not much time left, there's not much time left, there's not much time left...". Not even she is immune to the effects of Nightmare City. The Nightmare Casino that replaces it in version 13.5 is much tamer and more humorous by comparison, but it's also made clear that spending too much time there is not good for your health.
Princess Melanie, ruler of the Bad Future timeline in Chapter 12. In the wake of the catastrophe that destroyed nearly all of the doomed timeline's world, she decided that she wanted to rule over the ashes. To that end, she sent the Pyriahs to kidnap every survivor they found so she could make them her subjects. She destroyed all the landmasses she could so that the survivors would have no other option than to live on her island, and gleefully talks about killing those who don't obey her. This is made much creepier when you actually meet her and find out that she is a CHILD. She is also Melia's counterpart. The worst part? If she and Melia make physical contact, Melanie's mind proves stronger than Melia, merging the two and destroying any chance anyone had of saving the doomed timeline, and making her powerful enough to kill Madame X.
Where Love Lies reveals some horrifying things about the game's backstory: the fires in Gearen City and the Wispy Tower were both intentional and intended to hurt Kenneth by killing the ones he loved. The Wispy Tower fire killed a class of kids from Sheridan Village, while the Gearen City fire failed to kill Tesla and his other friends, though Jenner went missing, but broke up several families and did an enormous amount of damage. Kenneth himself was on the receiving end of so much shit that it's no wonder he had his emotions suppressed.
In the days leading up to the release of Version 12, Jan and Zumi's posts on the Dev Blog thread began to glitch out more and more as the version became closer to being completed. The text resembled something like Zalgo, and the words 'Fiat Lit Inn Or' (an anagram for 'infiltration') were repeated over and over. Both Jan and Zumi would also post gifs of glitched ghostly faces, which just made it worse. Zumi's last post in the thread being 'uh oh' did not help in the slightest.
Hiyoshi City in the past was a thriving town full of people. Hiyoshi City in the present... is Zone Zero, a desert wasteland full of abandoned buildings, where the people were turned to stone. It's implied that Storm-9 was the cause, but the effect is terrifying. Worse, when you go through Zone Zero, the player's name is still on their hospital room- when you went back to Hiyoshi City in chapter 13, you were there merely days before Storm-9 hit.
In the days leading up to the release of V13, Zumi put up posts from the perspective of an SPU delivery guy on the Rejuvenation forum. Each post talked about the player being sent a strange, moving package from the Puppet Master. When the image is clicked on, it sends you to a tumblr page with a riddle. When solved, you get some freaky, distorted gifs featuring a cryptic phrase in childish purple handwriting. The third is the worst, as it has the lovely addition of a gif of Saki either tied to or suspended in front of a picture frame with puppet strings.
In Chapter 15, Melia and Nim go through a series of rooms that were previously occupied by people who'd tried to host the Archetype's power and failed. Each room has a record of their last words, which just get worse and worse. Two tried to host the Archetype's power, were rejected and the rejection left them mortally wounded, two successfully hosted it but died from Genesis Syndrome, and the last two hosted it and died from wounds incurred during testing. At least one couldn't sustain the barrier against the gatling gun.
Saki's Nightmare Realm has her seeing visions of the mysterious duo dragging herself, Adam and Valarie into the pods that wiped their memories, intercut with still, grainy, black and white images of Saki's face, only with hollow pits for eyes. Later visions have the images look like Saki's face is melting.
Lavender's Nightmare Realm is not much better. It involved her being trapped in a space station, trying to escape a psychopathic Risa that chases her around and tries to attack her with a massive glaive and laughs through it all (Keep in mind: She doesn't attack her Pokémon, she attacks Lavender herself.) while saying things like 'Isn't it fun? Fun to run?'. Oh, and did we mention that sometimes she can teleport right in front of her with no warning whatsoever? The whole experience feels like something lifted straight out of Dead Space or Alien: Isolation.
The otherBad Future seen during the Paragon/Renegade Chapter 0 where the Xen HQ raid went horribly wrong. It's a completely desolated, cold, barren, constantly-shifting world with no color, where time doesn't even seem to pass anymore and the only people left are Melia and the Interceptor's host (Keep in mind, it's not you. It's the character whose body you're inhabiting, who seems to have regained control at some point). And they spent six years wandering this endless wasteland with no end in sight. There are no other people, no Pokémon... Nobody but them. And while in the Paragon route you're eventually treated to a small glimpse of hope... In the Renegade Route Melia finally ends up crossing the Despair Event Horizon and decides to kill her only friend in cold blood with a crowbar. The last thing you see before returning to the present is a creepy shot of Melia, brandishing said crowbar and a massiveSlasher Smile. Say goodbye to Melia, and hello to M2.
Oh, and said scene is not just a cutscene. The game lets you try to escape from her, but the area is completely closed off. You get to play your own murder at the hands of your best friend, who takes her sweet time bashing you with a crowbar and laughing about how your blood is the first colorful thing she has seen in years.
Making things better/worse is that THIS Melia ends up switching minds with our Melia on the Renegade route with no one the wiser except for the interceptor, and she's out for blood. Including yours. But the player character turns this around and makes a Deal with the Devil with her, she'll be able to get revenge on those who wronged her in the previous timeline, and in exchange, the player character gets her help in their plans to bring destruction to the world. Though she is an ally for now, it's clear M2 isn't all there sanity wise, to the point of having Literal Split Personalities that come about with no explanation, and as Laughably Evil as she is at times, she very much is still out for the player's blood. But M2 learns painfully at the end that she's not the devil in this deal, the player is.
The Renegade Interceptor. Yes, you during the Renegade Route make the above M2 look like a saint in comparison. Just through Karma Files you end up committing such vile acts like hunting down the Lake Trio and brutalizing them to the point where they've got no choice but to give you the materials for the Red Chain, use a spell called End of Night not just to kill your opponents, but outright erase all memories that everyone had of them, effectively deleting them from existence (Two of those people being Talon and Amber, one of your friends and your surrogate sister), cause an explosion on top of GDC's Central Building, the death count seen in the news the following day being in the thousands... By the end of it all, even M2 is thoroughly horrified by everything you've done so far, and while she tries to give you a "The Reason You Suck" Speech you effectively silence her by telling her that you feel no remorse for anything, that you could have killed her from the start and didn't even need her help to begin with, and call out her bluffs and her tough talk by confirming that she's completely and utterly terrified of you and what you're about to do to the world. Essentially, the Renegade Route Protagonist gives Madame X a run for her money with how cold and ruthless they are.
Eizen, a new character introduced in Version 13.5. He's Matthew's assistant, studying 'inconsistencies' in the world- things that used to exist in previous versions, but don't exist in the current version. Eizen is very aware that he didn't exist before this version, and that there is some weird shit going on, and he also happens to behave in some very... disturbing ways. He comes off as either already being insane or having gone insane from what he knows, and it's not pretty.
Surprisingly, even the Paragon Route has one. If Karen's not killed at Castle Zygara, then you and Melia get her to fall into the Voidal Chasm. To make matters worse, only the two of you, Alexandra, Damien and Ryland are the only ones who know she's down there and Alexandra's the only one who wants to get her out in the near future with Damien and Ryland wanting to wait until Team Xen is beaten to get her out. Either way, Karen's going to be in the Chasm for a long time...
Hazuki's sidequest has her and the player/Nymiera entering an old factory and saving some kids. At the end of the quest, you're forced to watch as the kid you can't reach is 'dissassembled'. While conscious. All the player sees is the screen turn red and blood everywhere afterwards, but that's more than enough to give anyone nightmares.
Eldritch Abomination doesn't begin to describe it.