Hi first-time poster here.
I stumbled upon a YouTube video listing out some very imaginative conspiracies people conjured up for the World of Pokemon. While I did come across really silly fan fiction, as well as a number of the more well-known ones in the past, there were several that caught my attention.
NOTE: Please refrain from reading if you don't feel comfortable with creepy content
To list a few:
The 3 Regis learn Hyper Beam at Lv 89, reference to the A-bomb Fat Man which was detonated over Nagasaki August 9, 1945.
Although Claydol learns Explosion at Lv 55 and Lv 72 for Gen 3 and Gen 5 respectively, it is Gen 4 when Explosion is learnt at Lv 86, possible reference to the A-bomb Little Boy dropped on Hiroshima August 6, 1945. Apparently with the jump from Gen3 to 4, moveset changes only apply to Claydol and legendaries from Gen1-3.
Victini - possible reference to Churchill's Victory sign, or Children's Peace Monument (http://www.pcf.city.hiroshima.jp/virtual/img/irei_img/tour_16.jpg) aka Children of Hiroshima Statue. Pokedex entries also hold a possible metaphorical reference, implying whoever has their hands on this infinite source of energy is assured victory, reference to the A-bomb.
And one I was more baffled by. Apparently:
In Diamond/Pearl, there is a book in the Library (presumably Canalave Library?) which says that "昔、人間とポケモンが交わった。" which literally means, "In the past, humans intersects with Pokemon" and the "intersect" could be synonymous with "keep company." However, in Japanese, the verb that describes this "交わる" can also commonly mean "to copulate," or "get in bed with" to be frank. I don't have the game anymore so I can't verify this, and I doubt any non-Japanese version would be unsuitably explicit lol. But think of all the human-like Pokemon. Like Jynx etc.
The more well-known one concerning Gengar and Clefable:
They share many similar physical features, as well as Gengar being known as the shadow Pokemon... but whose shadow?
This creepy one about Parasect scares the brown stuff out of me:
The reason Paras's eyes turned blank/ hollow/ pupil-less upon evolving into Parasect could be because the Mushroom on its back more or less sucked out every bit of life from its host (the orange bug underneath.) You could say the orange thing is dead, but the Mushroom is the real Parasect. This is supported by multiple Pokedex entries. And then remember where Paras were originally found? Mt Moon, where the alien Pokemon Clefairy call home.
Humans (might) eventually become Pokemon:
See Pokedex entries for Kadabra, Yamask, Spiritomb, Froslass, and somewhat related, Shuppet and Banette. Also, Bill turned himself into one during Gen 1 :P
And the last one I'll mention for now, possible evidence that the Pokemon World is a future version of our world:
The Pokedex entry does say, it is shaped like ancient writing. It is unknown whether they or the writing came first. Judging the Unown are basically the 26 Latin alphabet with the extra ! and ?, I think I'm pretty certain it's a real world reference in any case. Of course, other evidence include the several Pokemon regions introduced are all based on real world location.
Just sharing a few ideas that you might have or might not have already known :)
Most references came from /watch?v=irGAi3THt1w although obviously this isn't the original source.