And just to hammer the nail in further, one NPC asks you if you were on the train and says "so was my fiancee" before awkwardly ending the conversation. If that was too subtle, in earlier episodes she said "you were the lucky one" as well.
Dr. Sigmund's Orphanage of Fear. All the kids there are terrified and cannot wait to turn eighteen, because he won't let them be adopted and won't let them leave until they're legal adults. Why are they afraid? He tortures them with electricity in his "therapy" sessions.
Heather ends up there after her father dies, and he immediately marks her as his next "patient". As if she hasn't been through enough. Made even worse since Corey asks you to look after her, and you failed.
His speech when he seizes her is even worse. Despite Heather's repeated refusal to go anywhere with him, he essentially kidnaps her, sounding the whole time like a child molester about to drag her into his white van.
The scariest thing about Dr. Connal is not the torture he puts his patients through, but rather, how monolithically certain he is that he is doing the right thing. The man is insane enough to think that he's torturing those children for their own good!
Talk to people in the Obsidia ward during the attack. One crying girl will be too afraid to go outside because the street collapsed beneath her boyfriend's feet while he was walking next to her. Luckily, he survived, and once you get access to the depths of the Railnet system you can rescue him and reunite him with his girlfriend.
In the Mod Pokemon Reborn Hardcore, things get even worse. After his death, you can start a sidequest in which his ghost tells you to meet him in the place where you outed him, and tells you to "bring the ring". When you go there, he chews you out for bringing his own ring (used to catch his Pokemon) instead of Heather's Ruby Ring, and reveals the main purpose of bringing you here was to kill you. When the Player Character tries to run, they get cornered by the remains of his team, and Corey summons a swarm of Koffing to kill you with corrosive mist, attempting to murder you with his patched-together team! Somewhat mitigated in the end with The Reveal that it's not actually Corey's ghost, but his Haunter, who blames you for its master's death and wants revenge.
Shade's gym. It's an old power plant with no power, so it's pitch black inside, except for the occasional flicker. The music there is a low, menacing tune similar to what you find in Lavender Town and doesn't change when you encounter wild pokemon. To get to Shade, you have to stumble your way through the darkness, lowering the doors with terminals, and every time you activate a terminal you see how someone died. One girl getting attacked by a Garchomp, another being decapitated, Corey committing suicide...and the less said about Shade himself, the better.
And then there's the fact that his Gengar is named after Corey, whose body he collected.
Those "visions"? Those don't show how someone died, they show how someone will die. The girl being killed by a Garchomp is Kiki, who is indeed decapitated by Solaris's Garchomp while trying to stop him from erupting the volcano. And later on you have to see Amaria jumping down a waterfall because Titania admitted to faking being in love with her, ironically to help her with her apparent depression.
The PULSE machines. Just three of those things were able to destroy half the city with just Tangrowth. Imagine what one could do with, say, a Gyarados or a Tyranitar. Or even better, imagine what a whole army of Pokemon hooked up to those things could do.
The prototype pulse machine forcibly evolved a Magneton into a Magnezone, which isn't all that horrifying except for the fact that in the pokedex, it is said to be impossible to do artificially. Its creators, on the other hand, went through the exact same process, becoming ZEL.
Using a move of the same type as the field usually strengthens in, with the game saying "the murk added to the attack" (or something). Use a Poison-type move in the Wasteland, and the game tells you "the waste joined in the attack". That place is alive, and it's not friendly.
He's smart, cold, calculating, and has no qualms ordering his Pokémon to attack and kill defenseless humans. What Pokémon is it? A Garchomp—you know, the thing that Smogon banned to Ubers for being stupidly overpowered. And the game is not shy about showing how badly an ordinary human fares against it.
He orders Cal to throw Kiki's Medicham in lava. Imagine how traumatizing that would be for Kiki.
The scariest thing about Solaris, though? HE'S JUST TEAM METEOR'S DRAGON. The true leader of Team Meteor, Lin, is arguably even worse than Solaris! During the Enemy Mine situation in Team Meteor's Tanzan Mountain base, she not only sees right through Sirius' lie that the Player Character is a new recruit, but also knows right away that you're responsible for the subsequent attack on the base by Saphira and her Steelix! To give you an idea about how feared she is: EVEN SOLARIS IS RELUCTANT TO GET HER INVOLVED.
Lin'sfucking Hydreigon. That motherfucker's strong enough to stand up to Ame's- the Champion's- Alolan Ninetales. Which is an Ice/Fairy type. That is, it's a fucking Dragon-killer, and yet it couldn't take down that Hydreigon. And the implication that it ate Ame's head doesn't help.
Oh, yeah. Those methods of torture? Adrienn gets burned, Victoria gets shocked, and Arclight gets an eye ripped out.
Even the hideout where all of these events take place is designed to make you feel pain: The whole place is riddled with unavoidable tiles that develop electrical shocks to the protagonist every time they step on one of them. Again, they're unavoidable. And you have to step on several of them before reaching the end of the puzzle. And worse: They hurt your Pokémon too. It's very clear that Lin doesn't just want to kill you: She wants to see you suffer
Some of the custom shinies look a bit unverving, for example, Aegislash, Kecleon, and Vivillon. To elaborate, Vivillon has a demonic aura around it, Aegislash is splattered in blood, and Kecleon is almost completely invisible.
As of Episode 16, Aegislash's shiny form is now different from the above.
That giant fucking Steelix that causes all the earthquakes in Chrysolia.
At many points of the game, you'll see an Absol starring or yelling at you. Let's just remind that Absol is known to appear when a disaster is going to happen...
The Type: Null sidequest added in Episode 17. Dear lord, the Type: Null sidequest... It esentially involves you wandering into a hidden lab on 7th Street where, after battling the head scientist there, you're tasked with fetching certain Pokémon so she can use them to put together Type: Null's main body. That's right: You're handing your own Pokémon to this insane woman so she can tear them apart and fuse them together. And two of those mons you have to hand out, Luxray and Unfezant, are fully evolved so you have to train them at least a bit before sending them off. And after you do that? Type: Null, still having the memories of the Pokémon you handed out, lashes out against it's creator, killing her before deciding thathe wants to kill you too.
If you go down the story branch in Episode 17 where Lin tricks Titania into killing Taka, things for the rest of the episode start as Tear Jerker, but then quickly become equal parts that and this when you go to get Amaria's badge:
First, when you find Amaria in her gym, she quickly greets you and then runs off underwater. Of course, since you need her badge, you have to follow her underwater, where she eventually drops her cheerful act and traps you in an underwater room, leaving you to drown. Thankfully, Titania is able to save you, but if she hadn't come along...
In the aftermath of that, Amaria drops all pretense of civility and goes full-on Yandere, with nothing but pure, undiluted hatred towards the player for causing Titania to leave her. On the story route where Taka lives, she normally maintains an attitude of faux cheerfulness, but in this route she outright makes death threats and stays in a state of Tranquil Fury for the entire battle. Oh, and the fight ends with the implication that she's going to kill herself for real this time. This is perhaps exemplified best by what she says when she sends out her last Pokemon on this route: