Spoilers are unmarked!
- The beginning of the game itself. It shows a black screen, with a storm sounding in the background. There's a ominous dialog between two people, one telling the other to hold on. Then, the other person screams, with a large thunder noise/teleporting noise.
- The first time you have a vision can be freaky, especially if it's the first time you play the game. You're just talking to Azuril and Drowzee, then all of a sudden the screen flickers a bit. Then, cue the Scare Chord slashing noise, when all of a sudden the screen goes black, and the screen gets cut in half diagonally, showing you a soundless scene. This keeps happening throughout the game, but at least you'll know what will happen.
- Piplup's first vision in the anime special, at the very least, isn't near as nightmarish; it's just Sunflora picking out the team's gear for the trip. The second vision, on the other hand... well, let's just be glad Piplup was there to warn Chimchar and Sunflora that a bridge would give way.
- The Dark Future. ALL. OF. IT. This is easily one of the bleakest moments possible in a Pokémon game and the sentiment is not putting it lightly.
- In the Future, the sun never rises and time never passes. Primal Dialga is top dog. Thus, if you die, you will be stuck in that dying state for eternity. Given the fact that the world has become morbidly peaceful from the cold, still, lifeless silence that comes with the destruction of time itself, death is more welcome than trying to survive and eventually going insane from the dark, depressing atmosphere.
- Soon after you and your partner are dragged into the Bad Future, you're set up for execution. They tie you, your partner and Grovyle to pillars and about two or three of them gang up on them and use their Fury Swipes attack until death eventually occurs. And it's not a quick and easy sort, either - the method involves Sableye using Fury Swipes, meaning that you would've been torn to shreds by their sharp claws. Fancy being stuck in that state for all eternity, or worse, dying there.
- The Future Spiritomb in general. Not only does he torture Grovyle, he does the exact same thing to Celebi during Special Episode 5. Grovyle being tortured by that Spiritomb, which went up his nose, and the expression of pure agony on his face. It really makes you wonder what that Spiritomb was doing to him to cause him so much pain. Makes you glad that you defeated him.
- The future Dusknoir is a disturbing villain. Imagine T-800 meets Time Police trying to kill you just to get his horrific Crapsack World afloat, and you get the big picture.
- The thought of being hunted in a dark, future world by terminator-esque time police hunters is not a pleasant thought. The thought gets even less pleasant when your partner warns that Dusknoir could come back to the present and hunt you down... meaning he could easily chase you down again, meaning you're not safe ANYWHERE.
- You can turn around and talk to your teammates. In the fifth Special Episode in Sky, Dusknoir joins you (playing as Grovyle) for a while. If you turn around to talk to him, sometimes he says "Feeling nervous? Having your back exposed to me...". This is your first hint that he's the traitor.
- Dusknoir's backup plan in Special Episode 5 involves literally destroying Grovyle's soul, possessing his now-empty body, traveling back to the main time period, befriending the Guild members, and then destroying them in one fell swoop. Of course, he doesn't thanks to a foreshadowed Heel–Face Turn, but the implications are not good at all.
- Crossed with Tear Jerker, but in Explorers, your character can and will die. The game works hard to get you to imagine you truly are the MC in the game and then it kills you off, and you watch other characters mourn over you. Yeah, you come back, but still.
- Consider how things must seem from Azumarill's point of view. Just think about it: You have two darling children, your pride and joy. But then you get sick. So sick that you're bedridden and can't take care of them. Your dear, sweet boys comfort you as best they can, insisting that they can run errands for you and take care of things while you concentrate on getting back on your feet. And you might be a bit leery, but you've got to trust them. And besides, you know the town is safe. it's a pretty close-knit community, and you trust the shopkeepers and the locals enough to know they'll look out for your kids. But despite all that, your children are still abducted in broad daylight, right in the middle of town, by a seemingly friendly and helpful stranger who singles out your youngest for his own nasty intentions. And all this happens while you're so ill you can't do anything about it, and you only find out after it's all played out. Somehow the fact that the abductor is a Drowzee makes the tone of the whole situation a bit creepier, somewhat funny, or a little of both.
- Azurill's nightmare was creepier than it could've been. There's no food, your hunger increases faster, and there are Pokémon to fight in his dream... Not to mention the fact that the song that plays in little Azurill's nightmare
is disturbingly calm and sounds like a creepy remix of Heartwarming, the song of Azurill and Marill brothers. Pay attention to just which species of Pokémon are in the nightmare — among others, Wigglytuff, Chansey, Spoink, Spinda, Croagunk, Skitty, and Meowth — All of these are either friendly residents of Treasure Town or members of the guild, or Pokémon the player and the partner can potentially be. Yep, in Azurill's nightmare, his friends are out to kill him. Just the fact that almost every Pokémon in the dungeon are cute 'Mons generally associated with happiness and fairies (Many being retconned to Fairy in Gen VI) adds a weirdly disturbing aspect to it. - The misspelled items (such as the Oren Berry) in Sky. Imagine your character getting hungrier and hungrier every move, starting to lose HP. You eat those items to keep your hunger calm, only to realize that they nailed a status effect on you. Then, if you dare, you can eat the X-Eye Seed.
- There are some dungeons, particularly the Northern Desert, where the cracks on the walls are shaped like certain holes in a certain story...
- The music from Limestone Cavern in the Team Charm special episode really sends tingling chills down the spine.
- Depending on who's listening. Many people find the track calming.
- While on the topic of the game's music, the tracks In The Future and Planet's Paralysis are quite creepy.
- It may or may not have gone unnoticed, but given the fact that you and your partner were described as badly hurt by the Guild members after your battle with Grovyle, it's implied that had Dusknoir not stepped in, Grovyle could have easily killed both you and your partner.
- The fact that EVERY SINGLE BOSS has the desire to murder you, and none seem to have any problem with it. Even Team Skull at the very beginning of the game because your partner has a weird rock. Not to mention the Trio of Protectors (Mesprit, Uxie, Azelf) will basically do anything to protect the time gears, Uxie summoning a Mirage Groudon, while Mesprit prefers up and fighting you head-on, and the clan of Electric Pokémon in the Amp Plains just want to kill you for stepping on their land. Even after you defeat them all, they still want to slaughter you and your partner! And they would've, too, if Dusknoir hadn't stepped in. And that is just in the first half of the game. The second half and post game is far darker. Alright, Azelf doesn't, but played straight for everyone else. And then we have the Dark Future, with Spiritomb. And then the Hidden Land and Temporal Tower, with Dusknoir and Primal Dialga. The Graduation Exam is a nice break from the death, but then we have Froslass, who wants to freeze you like she did Scizor. Next, there is Cresselia (actually Darkrai), who attacks you after Azurill's nightmare. And then there is Palkia in the Spacial Rift, followed by a second illusory Cresselia who try to erase you from existence, with you only being saved by the actual Cresselia. Then there is Darkrai, the real one. So about ten bosses all want to kill you.
- Darkrai is easily one of the most horrific villains in the franchise. Ever. Unlike the usual Darkrai that's portrayed as misunderstood and maybe even heroic with a horrifying and uncontrollable self-defense mechanism, this version's Darkrai isn't. He's a cunning, ruthless nightmare master who's behind almost all of the above and admits it. He also sent poor Azurill into an infinite nightmare just to draw you in and convinces you and your partner to kill yourselves for the sake of the universe, and his plan is to send the world into an infinite nightmare so that he may rule. His first attempt was the bad future, in which he essentially corrupted a god. He then tricks another god into going after you and lures you into a final battle in which he traps you in another unsettling nightmare and gangs up on you.
- The fake Cresselia. Initially seeming like a gentle figure, this malevolent...thing is here to tell you to commit suicide, makes multiple attempts to murder you, tries to get Palkia to do it, then when that fails, tries (and succeeds) at mentally breaking your partner and making them accept their demise. It takes the real one to show up and expose that as Darkrai. It's made worse by the first time one shows up, that was likely the real one muttering about catching Darkrai, making it seem like she's here in the dream to warn you, but then this Out of Character and unsettling impersonator shows up to be as harsh and mean as possible.
- Right before fighting him, your partner seemingly has a Face–Heel Turn and asks you to join them. They clinch it by saying "The world of darkness is going to be wonderful." And then they follow-up by saying "Darkrai won't want just me... he'll get rid of me..." Despite that's just an illusion, the idea that your trusted partner, who's been to Hell and back with you, just gave up and went over to the Big Bad and begged you to rule with them because they know that without you they'd be killed, but they weren't going to go back on it is really nightmarish and it's hard to tell that it was just a nightmare. Not only was it scaring you as the character, it was scaring Cresselia as well.
- During the battle near the end, Darkrai can sometimes stand there and stare at your character, watching carefully. Though this is a normal consequence of the Status Checker IQ skill, it takes on a new meaning here.
- Near the end of the fifth Special Episode in Explorers of Sky, Dusknoir has a Heel–Face Turn and rescues Grovyle from a trap he led him into. Primal Dialga's response is to give a No-Holds-Barred Beatdown to Dusknoir. What makes it particularly striking is that cutscene violence in the early PMD games is typically limited to one, maybe two strikes. Primal Dialga hits him four times, and the contrast to the usual way makes it seem brutal, even with the limitations of the 2D sprites.
- Although it’s fan-made, this video that showcases a possible Downer Ending for the game provides heavy Nightmare Fuel, as it shows the cruel reality of what would happen if you and your partner failed to stop the paralysis. The worst part is seeing the Guide terrified and unsure of what’s to come (topped off by the sky being dark and the lack of music), and the black-and-white text at the end saying that no one survived. Thankfully, the game has no bad ending and allows you to Take Your Time, but it does make you feel somewhat guilty for all those times you spent in Treasure Town grinding for Dialga when you should be in Temporal Tower.
