I'd argue for Kanto, the implications of the Mewtwo experiments are a close second. The Pokemon mansion has a lot of genuine sci-fi horror elements and are generally unsettling especially with the tone and themes of pokemon as a whole. Pokemon genetic experimentation is basically the opposite of what the pokemon journey is meant to be about.

Um for X and Y, it's only told and not shown because Game Freak probably thought it was too dark to show, but Team Flare 100% qualifies for the darkest moment of this game as during the climax, they literally attached Pokémon to the stones of Route 10, slowly draining their Life Energy, causing the Pokémon to scream in agony as they're slowly dying.

We know it happens as after they're stopped, we're told by Dexio and Sina that they were able to free the Pokémon from the stones, and their agony is hinted at by one of the grunts blocking the path to Route 10 during the climax as he tries to convince himself that he "doesn't hear the cries".

It's far darker than a random Ghost Girl that shows up only to leave basically immediatly.

For X and Y I'd actually argue AZ's basckstory is the darkest moment. Him creating a superweapon and firing it at an army of Pokemon and people is really messed up and the eternal life he and floette are cursed with after that are also dark.

Everything about Zinnia. She's much deeper and darker than people give her credit for, literally dealing with suicidal ideation, which is quite surprising for Pokémon.

For Gen 2 I feel like Cinnabar Island is up there

I feel like AZ being cursed to live out the next 3000 years alone and abandoned by the one Pokémon he cared about is a pretty dark and tragic moment in the kalos games

Lavender town definitely made me feel how real Pokemon are and that they are living beings.

In ZA, for me, apart from Az dying. It's the old widowed woman sidequests that starts in the base game looking for her ring and then, in Hyper Dimensions, her husband giving you a letter for her. At first it'a odd because this implies it's an alternative version of his husband trapped, but once you know each dimension is the dream of a collective whole or a specific set of people that meant she still wished for him to be alive or had still some grief but the cart eased her mind gave her true peace.

I suppose this is more "heartwarming" than dark, but I'm a bit surprised you had nothing to say about the old man in Anistar City in XY. His wife recently died and asks for you to give him a low-level Pokemon to keep him company. Once you reach the postgame and return to his house, you will find that he died as well.

For Johto I would say the Burned Tower that, well, burned down while three beasts were trapped in it. Ho-Oh reviving them turns it from staying super dark, but reviving still means they had fully perished dead first.

Pokémon is no stranger to dark moments and messed up implications when it comes to its worldbuilding and characters. I honestly think that it adds to the games because, while I don't believe that they should always lean into this direction, it gives the player an unsettling reality check : that even in the bright world of Pokémons and excited adventures, tragedies, unealthy obsessions, disturbing events and unhappy endings exist. At least that's how I see it anyway.

Not gonna lie, the Cubone/Marowak event in the Let's Go games absolutely broke me.

I'd like to say another dark part of X and Y is the lonely old man in Anistar City. Not only is he lonely with his wife passed away, but if you give him a low level pokemon and return after beating the league, he passes away too. That always hurts.

I honestly think the Darkest if not the saddest scene in the whole series is AZ’s backstory during X and Y and it reads “he was given a tiny box” and we see a coffin with Floette inside it then we see all the pokemon graves after.

Can't believe Lusamine's frozen Pokemon collection didn't even get a mention... Might be the darkest moment franchise wide.

For Sinnoh, I think the creation of the Red chain was my pick. Literally torturing the Lake trio just for them to create a red chain to bind Dialga/Palkia, while they are suffering, is my pick for darkest moment

For Kalos, I think an extremely overlooked detail is how Lysandre is powering up the ultimate weapon. Literally using the statues on route 10, taking their life essences which was implied to impact the pokemon on the route, was something else. Even one of the grunts pretending they are not hearing the screaming, I think it is very messed up and the darkest moment in possibly the series.

Galar I would say Bede getting outcasted by Rose for his frankly stupid plan, being chided and kicked out of the league challenge, plus Bede not having a family member to look up to besides Rose, really sent him spiraling. Plus at the same time Hop having a major identity crisis and nearly throwing in the towel... I am grasping at straws.

i'd say emma is pretty sad

Mount Silver in general deserves mention for GSC. There are extreme safeguards about the place simply because the Pokémon there are too dangerous. Ursaring being a prevalent species in Gold makes the hazardous predator element feel much more uncomfortably real. Red is found at the mountain's summit, completely isolated, and says nothing before mysteriously vanishing once he's defeated, with even his mom saying she's worried about his whereabouts.

Black and white has kyurem eating people in the lore

Most common denominator always seems to be that surefire contrast to the lightheartedness of these games: death, or just spirits. Lavender Town and the restless Marowak soul, the ghost girl of Hammerlocke finding closure, the gravestones of Kalos Route 10, the reveal of Arven's professor parent and even the moth Pokémon/white flower Floette foreshadowing in Area Zero, they all deal with something not easily approachable. Even the Hex Maniac ghost of the fighting dojo in Lumiose could count, since it's never elaborated on, is apparently a recurring phenomenon, and it doesn't seem dismissible as the doing of a Ghost Pokémon's either. Even to lesser extents would be some of the Ghost Pokémon, if Pokedex entries are to be believed, like Litwick, Drifloon/Drifblim, Yamask, and such. I love these moments, they fire up my imagination so much.