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Nightmare Fuel: We Are All Pokémon Trainers
We Are All Pokémon Trainers is an RP that is generally lighthearted if at times slightly darker than the source material. However, due to the freedom afforded to it by virtue of it being a fanwork, it can be horrifying in far more explicit ways than the source material.
The fact that 'M managed to have Steven Stone under his mind control for at least six years before the start of the RP's story, and no one knew.
The way the Mummy ability of Yamask and Cofagrigus is shown to work in the RP: Covering the victim in ghostly bandages, preventing them from moving around too much and which can spread to other Pokémon that make physical contact with them. The Cofagrigus is also shown to be able to use the ghostly wrappings to manipulate the bodies of their victims, and can use them against their own team mates against their will that way.
Eliza, Jane's Jellicent, who can at times show a disturbing lack of mental lucidity.
The fate of the children 'M abducted from the daycare, being forcibly transformed into Shiny Charizard 'M. The Glitch even mentions that he removed the vocal chords of the kids because he found their crying annoying. Luckily they managed to be reverted to normal.
Some of Fool's descriptions of her life in Pinwheel Forest before leaving are not for the fainthearted. They include:
Explicit descriptions of interspecies warfare between the Panpour and Pansear populations.
The reason Fool left in the first place, murdering the higher ranked Simipour troop members she and Michelle were supposed to "consummate" with, and being forced to flee or face mauling by the rest of the troop. It was so bad that Tagg is the only J-Team member who knows the full story.
Majora!Fool and the Discord-inspired chaos he caused.
Linux's evolution: He got glitched by the Invisible Shiny Bulbasaur, and got twisted, split, and warped painfully, turning him into an even-more-corrupted-than-usual Porygon-Z. In-universe, it wasNightmare Fuel for Alli.
The lowermost levels of PEFE HQ, home to deadly mutants such as the half human Scythermen and mostly unexplored.
While Cipher is already pretty bad in the actual canon, within WAAPT their explicit evil is increased immensely, such as through the onscreen outright murder of dissidents.
Cipher even became in-universe Nightmare Fuel to Sakura as well as Paranoia Fuel
Shadow Pokémon, living beings that may have been perfectly decent or even outright good mons being tortured to become living weapons that only live to hurt and kill others without feeling any sort of guilt or remorse for their actions.
Shadow!Duke is notable for being extremely sadistic while being in a perpetual case of Dissonant Serenity, he utterly curb-stomps Herbert's team while gleefully talking about torturing them himself, not only that, but he comes dangerously close to killing Herbert himself, the only thing stopping him from doing so being Alexia deciding to recall him before he could finish him off. Considering how he is normally, it's quite the terrifying change.
Perhaps the scariest thing about Shadow Pokemon is that they're immune to a conventional "I Know You're in There Somewhere" Fight, since their memories are locked away and getting through to them is impossible. Meaning that they'll quite happily beat former friends to death without hesitation.
Whatever the hell Cipher did to Shadow!Regina.
No one knows exactly what goes into the Shadowfication process, mainly because every Pokémon refuses to talk about what that entails. It's simply that utterly horrifying.
Diane's was shown in a post specifically marked due to how horrifying it was. It involved various forms of pain and torture that all are purely mental; although she received no actual injuries, she felt every ounce of suffering.
The first Cipher meeting, in which the operatives present casually discuss possibly murdering children (most of the J-Team) like how most people discuss the weather.
Kyrie is terrifyinglyinsane, and any time that this is demonstrated, like her dream or her attempted murder of Joseph is Nightmare Fuel for some.