This stuff really happens. Ain't no fanon here.
As per Nightmare Fuel policy, all spoilers are unmarked!
- Red and Blue had Team Rocket kill a Marowak when they took Mr. Fuji hostage, leaving the player to battle her vengeful ghost. Luckily, in the Let's Go games, she's calmed down by her Cubone child without a fight.
- At Celestic Town, a Galactic Grunt mentions a "package" that's going to destroy Celestic Town. It turns out to be a bomb which causes the Sacred Lake to evaporate. That's right, Team Galactic isn't just a crime syndicate, they're terrorists.
- Pokémon: Lucario and the Mystery of Mew, the movie featuring Lucario, confirms a terrifying fact: in ancient times, Pokémon used to go to war with their human trainers/soldiers, who used them instead of weapons. Considering what little of Lt. Surge's background is given and dialogue of a trainer in his gym "Gentleman Tucker", wars with Pokémon still happen in the present time. X and Y outright confirm it. There have been wars in the past, that Humans and their Pokemon take part in. Most likely, the only reason AZ didn't fight yet his Pokémon were enlisted was because he was King and literally could not fight, even if he wanted to.
- Escalation of the villainy of the various teams: Team Rocket were generically nefarious, but mostly dim and restricted to ordinary organized crime; Team Aqua wanted to expand the oceans, which would have drowned coastal cities, and Team Magma wanted to expand the landmass, mostly by causing a volcanic eruption, but both believed that their actions would benefit humanity. Team Galactic wanted to summon a godlike being in order to destroy the universe and recreate it: they wanted to end existence and create their own, supposedly "better" universe with Cyrus as the supreme ruler. In Platinum, the "perfect world" Cyrus wants to create is a "world without spirit". He wants to unmake the world, and purge it of all traces of individuality, emotion, knowledge, and thought. And even after defeating him and pacifying Giratina, he says that he has not abandoned his plans, and leaves with this ominous line: "One day, you will awake in my world. A world without spirit." Team Plasma wanted to confiscate Pokémon from their trainers so they could rule the world with an iron fist. Team Flare wanted to use an ancient weapon to wipe out all of civilization except their own. Finally, Team Rainbow Rocket is a compilation of villainy consisting of several key figures from the villainous teams of the first six games. Thankfully, Team Skull and Team Yell relegate back to being nothing more than ordinary street thugs.
- Team Skull being the villainous team of Alola gives Sun/Moon a lighter tone than any Pokémon game...until we learn just what's really happening at Aether Paradise and what Lusamine is really like.
- According to an old couple in Sunyshore City, "[Cyrus] was always like this, even at a young age."
- The vast majority of Team Galactic don't even know about Cyrus's true motives and the true nature of the world he wants to create: he's playing them all like fools.
- Cyrus is made worse in the manga: in Volume Two, he explains his plan to Hareta. It starts off reasonably calmly as he talks about "a world where there is no fighting and where everyone can live smiling." Then all of a sudden, he grips Hareta by the shoulders and blurts out that, for the sake of that new world, "The sacrifice of thousands, even tens of thousands of Pokémon means nothing!", all while sporting a Slasher Smile and telling Hareta that "We Can Rule Together".
- Cyrus' fate in the anime is perhaps more disturbing than anything he did in the games. Basically, he walked into the outer space of the new world that was being created, and the portal he used to do so then contracts upon itself before being destroyed by Dialga and Palkia. It's possible the whole thing went with it and he's dead now.
- To top it all off, Ultra Sun and Ultra Moon straight up state that there exists worlds where these megalomaniacs ACTUALLY SUCCEEDED IN THEIR PLANS. Just imagine how miserable life must be in the aftermath of their worlds.
- The Distortion World, known as the Reverse World in the 11th film. The idea of a world where gravity shifts under your feet may or may not be frightening to some people, but it starts to get disturbing when platforms hovering above an endless void disappear right as players try to step on them... and when very tall sunflowers grow backwards into the ground when approaching them... and when people behave oddly and then suddenly disappear into thin air. That, the dark color scheme, the Eldritch Abomination that flies overhead every so often, and the creepy music
add up to an overpowering feeling that this is a place man was not meant to see. - The fate of the Cinnabar Islands and Blaine in the original Gold/Silver: Cinnabar blew up, almost everyone who lived there has left, and Blaine's become a recluse — yet still a gym leader — in the Seafoam Islands. Thankfully, following the eruption, as remarked by one guy found in the Cinnabar Pokémon Center (as of the remakes at least), everybody got away from the island safely. The remakes also added a somber version of the once-cheery Cinnabar Island theme as the BGM. To clarify: Generation I, Generation III (both for the safe Cinnabar Islands), and Generation IV (ruins), complete with retraux Generation II counterpart composed from scratch.
- The Lake Trio, Azelf, Mesprit, and Uxie, can turn people into stone, take their emotions, or wipe their memories, respectively, as each one acts as the deity in charge of each aspect. And none of this can be reversed for one thousand years.
- Gold and Silver has the Lake of Rage before thwarting Team Rocket, as Gyarados — normally — are described as being unable to control their power, and so they go absolutely crazy with it, vaporizing everything around them until there's nothing left to violatenote . They have also exhibited tendencies that suggest they are drawn to violence and rage. Apparently, this change in temperament is thought to originate in a Magikarp's brain cells rewriting themselves upon evolution. After these premises, in Team Rocket's hideout, a creepy little Easter Egg melody can be listened to, thanks to the PokéGear radio: it's a transmission that Team Rocket is using to evolve the Magikarp into Gyarados involving plenty of scary sounds. Team Rocket is implied to have planned to take it even further by having it driving every Pokémon in Johto crazy as well, near populated areas. It's also explicitly mentioned that the Unown communicate using radio signals: Ruins of Alph is the only place to hear them, as that's where they live, only this time the scary noise can be listened to at will. It's not as hellish, as it relies much more on scary vagueness.
- One scientist found in Team Rocket HQ says:"If we turn up the power of our radio signal for broadcast... the very thought excites me!"
- One scientist found in Team Rocket HQ says:
- Pokémon: Diamond and Pearl Adventure!: When the heroes follow Charon and his goons into the Distortion World, they find not only a creepy landscape, but a creepy landscape littered with bodies. All the Galactic grunts are lying around with no signs of life. A moment before, they were screaming for help.
- The end-game of Ruby and Sapphire: while Team Galactic didn't get to trigger the apocalypse they wanted, Team Aqua/Magma did. Of course, the hero saves the day, but a brief Darkest Hour actually happened for real this time.
- In one chapter of The Electric Tale of Pikachu, Ash's Charizard is fighting Ritchie's. While in the anime he fights Ritchie's Charmander and falls asleep on Ash, in this manga he becomes violent to the point where he's using lethal force on Ritchie's Charizard. Ritchie is unable to call back his Pokémon and Charizard won't snap out of his rage, so Ash has to put him into his Pokéball. The scene is quite bloody.
- The part of How I Became a Pokémon Card when Dragonite tries to find his son. His eyes are glowing and he's destroying everything in sight. The military tries to kill him until a young Bill comes in and stops them.
- The ending of chapter 11 of Pokémon Adventures's Black and White arc is rather creepy. White jumps out of a Ferris Wheel while it's still on — though apparently, it's not that far up. As her Tepig just betrayed her, she's in tears — but she's lying down in an awkward position with Mind-Control Eyes.
- In one How I Became a Pokémon Card one-shot, the protagonist, Akane, is an orphan who was raised by Impostor Professor Oak. As his name says, he's an impostor of Oak. Nothing is verified about him in this man, and in the source cards, he's a Team Rocket member.
- In the Battle Chateau, you encounter Marquis Arran, who apologizes and says his master commanded him to attack you. And he never reveals his master's identity.
- There's a small segment in Pokémon Platinum that is often forgotten but ranks easily as one of the most unnerving moments of the series. Right after the second battle against Cyrus inside Galactic Hideout, you descend to the basement where the Lake Trio is held captive. Not only is the theme played there really unsettling, but you get to: 1) Talk with the scientists that worked on Cyrus' plan, and they are horrified with the results of the research; 2) Find the Lake Trio trapped in machines being apparently tortured and 3) Go through a wing full of huge pods filled with green fluid with... something floating inside. We never find out what the "something" is.
- Two segments in the (now defunct) Pokémon Learning League have some NASTY Realism-Induced Horror elements.
- In the "Cyberbullying" segment, Team Rocket (in a surprisingly cruel move) decide to target Zoey, posting nasty messages in an attempt to break her spirit and convince her to not only give up on Coordinating but give up her Pokémon. Let me repeat; Team Rocket very nearly broke a child's spirit simply for their own profit and it's implied that if Ash and crew hadn't tapped into the Learning League mentor du episode, it might have WORKED.
- In the Internet Safety segment, Dawn breaks a cardinal rule of safe Internet chatting and meets her new "friend" in person...only to discover it was Team Rocket all along and she's just walked into a trap meant to steal her Pokémon.
