Nightmare Fuel / Traveler

• Pierce is the story's first look at Team Rocket and he ruthlessly orders his Muk to murder Ash and his friends when they refuse to hand over their pokemon.
• Basically every appearance Mewtwo makes is horrific.
  • It's first appearance is destroying the S.S. Anne and killing thousands.
  • In it's second, Mewtwo easily takes on the Elite Four and dozens of ACE trainers, leaving most injured and several dead.
  • Mewtwo's third appearance coincides with the first movie and unlike canon, it's made clear that nearly every trainer that didn't reach New Island died. Furthermore, the initial battle against Mewtwo's clones is part of a cruel game. For each of his clones defeated, he'll spare one region of the continent from destruction, but Kanto is doomed regardless. Mewtwo also breaks a trainer's arm then fixes it to prove a point, buries Moltres at the bottom of the sea, and declares his intention to use the trainers who reached New Island as his lieutenants to conquer the world regardless of their consent.
  • Even after his sorta redemption, Mewtwo still performs horrific acts like stopping Ash's heart for thinking a colony of Metagross was more impressive than itself.
• Spiritomb qualifies in universe, giving off an aura of pure malice and dread. Making matters worse, it was created by unmaking 108 people and binding their souls together into a keystone.
• When sealing away the Unown, Ash has multiple visions of events to come that he will be involved in, two stand out. The first is a confrontation between a Behemoth and Leviathan, meaning Groudon and Kyogre are to awaken just as Lugia warned him. Next is a laughing a mad man attempting to remake the universe using Dialga and Palkia, alluding to Cyrus and Team Galactic.
• In-universe, Ash is filled with dread to know that Articuno's high priestess Haukea, who helped create the first Jynx through Human Sacrifice, is both still alive and aware of him and his connection to Articuno. When Ash asks if Haukea wants to destroy the league, his answer is "Does a blizzard want to bury a village?"
  • To give context to Haukea's age: Chinatsu, the Ninetales who fought alongside the first Indigo Champion over 1000 years before canon, stated that Haukea was ancient during the time of her grandmother.
  • When Ash meets the Jynx Haukea created, he has a vision of the ceremony that turn the girl into Jynx.
  • At one point in the tie-in, Lance briefly sees Ash heading down the same path Haukea went down under the realization of just how much Ash's journey has damaged him and vows to make sure Ash doesn't end up like the woman.
  • After the Greenfield Disaster, Haukea allows a news crew to interview her about her cult, with her Feather of Articuno exposed for all to see.
• Ash reaches out to Mewtwo in the aftermath of sealing away the Unown and notes that Mewtwo sounded tired and drained of energy when the pokemon refused to heal Delia's mind. A hivemind of Unown was enough to almost drain and defeat the World's Most Powerful Pokemon.
• In chapter 54, Agatha explains how her family attempted to merge humans with ghosts, creating insane abominations that weren't human, ghosts, or even a proper combination of the two. Eventually they used newborn children. When her family fell from grace, Agatha's grandfather used her, turning her into a perfect combination of human and ghost.
• The old parts of Lavender Town never see any true sunlight, even in the middle of the day. And at night, the streets are absolutely filled with ghost types searching for living to prey upon. As Ash walks towards Lavender Tower in the evening, he's quickly followed by a horde of ghosts looking for a moment of weakness to pounce.
• Lavender Tower is filled with hundreds of thousands of spirits who fill the air with their emotions, the air is difficult to breathe and even the power of the Feather is smothered. On the top floor is where the dead are cremated and is covered in a layer of ash several inches thick. Dwelling there is a ghost known only as Lavender, which is not a Ghost Pokemon, but the combined spirits of every single person and pokemon who has died in the town over the last several hundred years.
• While training near Mt. Chimney, Ash is left with a constant feeling of unease. When he finally manages to open himself up and learn what's bothering him so much, he's nearly burned alive from the inside by the power of Groudon, who's so massive that its body takes up most of the mountain range.
  • Having to report the information to Steven, who has a minor freak out before sitting Ash down to get an official report.
• Infernus is teleported into the depths of Mt. Chimney to train against the creatures there. Whatever was down there is stated to be completely unlike any pokemon anyone has ever seen and are powerful enough that they beat Infernus within an inch of his life. Slightly downplayed with the fact Infernus clearly had the time of his life.
• Flannery shows Ash a cave not far from Mt. Chimney which has a small tunnel branching off of it. Flannery admits she's never gone down the tunnel because it "feels like it wants [her] to enter". When Ash ventures within, he finds the remains of several hundred humans and pokemon within. All of them pointing towards a dais upon which a purple crystal sits. Ash eventually puzzles out that the crystal is the chrysalis of Jirachi, the Wish Maker. All those corpses and skeletons? They were lured there by Jirachi's aura promising anything they wanted, which kept them there until they died. The ancient Draconids so feared Jirachi's power that they used a tiny fragment of Groudon's power to etch a permanent warning upon the entrance to the cave, both in writing and in a psychic imprint. Even a completely benevolent Legendary like Jirachi is far too dangerous for mankind.
  • In order to reach the dais, Ash is forced to climb over the piles of corpses of those who also came looking for Jirachi. When he finishes his climb, he promptly throws up from a combination of nausea and horror. Upon getting ready to leave, he breaks down, begging for anyone who will listen to not make him have to do the climb again. Mewtwo, who already told Ash after the boy was almost absorbed into Groudon's consciousness that he would not help him again, takes pity on him and teleports Ash to the other side of the cave to spare him.
• During a mission to the Arid Zone to find out what's been attacking local people and pokémon, Ash finds an immensely powerful Spiritomb that assaults him and his team with telepathic waves of apathy and despair, very nearly convincing all of them to simply lay down and die.
  • While fighting Spiritomb, Ash is repeatedly shown visions of him dying and/or simply giving up: Giving away Nidoran to Pierce to save his own life, being smothered to death by Pierce's Muk, having his head bashed in against a cave wall, being frozen to death by Articuno, etc.
• Tobias. Whatever Darkrai did drove the man insane so that he refers to himself in the third person, has an unkempt appearance, and even Agatha refers to the man as an 'it' instead of a human.
  • When Ash tells Phoebe about his most recent encounter with the man, Phoebe's entire demeanor changes and she demands to know where he is. Apparently the League has been tracking his movements and don't consider Tobias to be a human anymore.
• Wes and his talk with Ash
  • Ho-oh revived Wes, but he is no longer a pure human and is just one of Ho-oh's feathers/human personae now.
  • When Wes tells Ash that he will be facing even more challenges and blesses his feather with some of Ho-oh's power, Mewtwo laughs loud enough to scare Ash.
• Ash and his visions. After sealing away the Unown, Ash has been able to see visions of past experiences from other pokemon or spirits. He even feels everything the originator felt physically and emotionally during the experience.
• Rogue Master Jacqueline Durand is able to get away thanks to her Malamar firing a Confuse Ray in Ash's face. Instead of trying to fight his way out of the temporary Distortion, Ash tries to explore it and comes across a pair of red eyes glaring at him. Ash unknowingly comes across Giratina in his pursuit for knowledge and is lucky that it did not try to keep him there.
• The Harbinger. It's apparently an Absol that takes glee in hunting down ghosts. An encounter between the Harbinger and Sidney leaves the latter quiet for a few days. When mere rumor starts that it is seeking out Ash to kill his Spiritomb, Steven immediately arranges for Ash to stay on Mt. Pyre, a place that it cannot come near.
• If Durand's information is to believed, Team Flare is basically running the Kalos region from the shadows.
• Sabrina mentions that she has attempted to locate Zinnia and tried to use her powers to find her in Kalos, but could only see Oblivion.