- 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. Luckily, everybody survived the attack and you end up getting to save them later on.
- The Dimensional Rifts. They are created with the sacrifice of a Pokemon, and they bring forth dark energy from the cracks between dimensions. While they can be used for mundane things like transportation, they are mostly used to revive the said sacrificed Pokemon into an undead abomination with horrible powers, unable to stop itself from rampaging. The only way to stop it is to kill it, but considering the pain the Pokemon is in, killing it is probably the nicer option.
- 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.
- Most of the Dimensional Rift Pokemon aren't too freaky looking... and then you get to the Dimensional Rift Carnivine. Eldritch Abomination doesn't begin to describe it.
- Angie's Villainous Breakdown. Unlike any other villain in the canonical Pokemon games, after her defeat in a Pokemon 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?
- It gets worse: as hinted by the end of V7 and outright confirmed by Jan, the Pokemon that was made into Angie's rift was a Regice!
- The Reveal in the Stinger of Version 6 that Crescent was evil all along. This lady can kidnap people with impunity and banish them to an alternate dimension, brainwash people into doing her bidding, and CHEAT DEATH ITSELF, and she's implied to be playing everybody to achieve her goals, possibly the one of the Prophecies. If what Geara and Angie did was any indication, then it's pretty likely that simply defeating her in a Pokemon battle isn't going to do much.
- The Stinger of Version 7 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 Up to Eleven. 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 (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 revamped "The Hidden Library 3" Sidequest in V9 is mostly funny, there is one disturbing bit: right before you enter the Unown Dimension, A GIANT UNOWN EYEBALL OPENS UP ON THE FLOOR.
- Goldenleaf Town. 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 Poke Mart, or the girl who implies that she killed an outsider for asking her out.
- 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 Crescent is immune to the effects of Nightmare City.
- Melanie, the doomed timeline's equivalent of Melia. She's a tiny child psychopath who, in the wake of the catastrophe that destroyed nearly all of the doomed timeline's world, decided that she wanted to rule over the ashes. To that end, she sent the Renegades 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. 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.
Nightmare Fuel / Pokemon Rejuvenation