The Pokémon world is one where 10-year-olds traverse entire countries on foot alone save for the company of semi-intelligent rodents and fish. Once you've accepted that, then suspending your disbelief about the Pokémon universe should come easy, right?
But there are plenty more mysteries afoot in the Kanto, Johto, Hoenn, et al regions of planet Pokémon. And just because none of the characters in the games or the various TV shows/movies seem to recognize the absurdity of their world, it doesn't mean we can't wonder at what the answers are to some of these big questions. Below is a list of what we think are the more significant mysteries are in the Pokémon universe.
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What is the inside of a Pokéball really like?
This may be the biggest mystery in all of Pokémon. These poor creatures--from the tiny Caterpie to the mighty Wailord--spend 99% of their days in Pokéballs. What's really going on in there? Do the Pokéballs administer a sedative? Are Pokémon forced into a chemical sleep state? Do they dream? Are they stuck in a never-ending nightmare until their cruel trainers deign to let them out into the sun for brief bouts of violence? Is that why they're always so eager to fight each other? Will The Pokémon Company ever answer these questions? Not a chance.
Why does every Nurse Joy and Officer Jenny look identical?
Scientists in the world of Pokémon have pretty advanced cloning technology. But cloning alone can't quite explain the mystery of why every town seems to have a small army of Nurse Joys and Officer Jennys. Allegedly these characters are simply all related, but who's really buying that?
It would be a dark episode that revealed the origin of the clandestine government cloning program that fabricated itself a never-ending supply of loyal public servants. That's one way to achieve universal health care at least. But the bigger mystery: why does everyone just accept that they're all twins? And can Brock really tell them apart, or is he just trying to get in their pants?
Why can Meowth talk?
Here's one that the characters in the Pokémon TV shows actually do acknowledge, though it's never addressed satisfactorily: why the hell can Team Rocket's Meowth speak human language? Granted, there are some Pokémon who can speak naturally, like the Slowking in the second Pokémon movie, and Mewtwo, who was genetically engineered to be incredibly smart (just like Nurse Joy and Officer Jenny were apparently engineered to be super weird identical twins).
The episode "Go West Young Meowth" asserts that Meowth taught himself to speak and walk like a human in order to win the affections of an attractive female Meowth, but there are so many problems with that explanation it's hard to know where to start. Here's an easy one: if it's that easy for a Pokémon to learn English or Japanese, why do 99% of them just repeat their own names ad nauseam like an entire animal kingdom of Hodors?
Can Ash actually understand Pikachu?
The little rat only ever says his own name, infused with various emotions and seemingly more grating with every utterance, and understanding it should be only slightly easier than trying to figure out what your cat is thinking. Yet Ash has in-depth conversations with Pikachu in which the rodent advises, praises, and even admonishes its trainer.
Other trainers can also converse with their Pokémon to varying degrees, though apparently none share the special bond that Ash and Pikachu have. It's a bond born of…what? Shared experiences and a deep love for one another? Or the delusional psychosis of a 10-year-old hobo who had too many imaginary friends growing up? We'll probably never know the truth.
Where is Ash's dad?
It's become a running joke that most of the protagonists in Pokémon, including the TV show's Ash Ketchum, actually have fathers. Their mothers like to assure them otherwise--"your dad was a great Pokémon trainer"--but it's a legitimate possibility that all these characters were conceived spontaneously, or judging by how Pokémon breeding works, popped out of eggs. This is a universe in which all life descended from a flying, hairless, pink cat, after all.
How does Pokémon breeding really work?
It seems no one really knows how Pokémon procreate--even the daycare people who hand you your little monsters' eggs in the various game. "We don't know how it got there!" they exclaim, and after a while you can't help but believe them. Mr. Mime and Klefki lay eggs? Geodude, the boulder Pokémon, likes to get it on with Vanilluxe, the conjoined ice cream cone twins? Game Freak has some 'splainin to do in this department, not that they ever will.
Does everyone eat Pokémon?
Unless everyone in the world of Pokémon is a vegetarian--and they're definitely not--then these people must be eating the Pokémon. Consuming animal flesh is an accepted part of real world society, but although Pokémon are clearly related to animals, they're definitely not the same thing. And although regular animals are occasionally mentioned in the games and anime, they're either extremely rare or extinct, having been supplanted by genetically superior Pokémon.
So is there a factory farm somewhere in Johto filled with Miltanks for meat? Does Grumpig taste better when served with apple sauce? Are Wailords being poached into extinction there too? These are questions most Pokémon trainers would probably rather not think about.
What really goes on at Pokémon Centers?
Every major town has one. There's a Pokémon Center before you face the Elite Four. They all have their own identical Nurse Joys, but that's not even the creepiest thing about them. What really goes on at Pokémon Centers?
It's well-established that Pokémon can die. But somehow they don't die in battle, even when Bulbasaur is consumed by fire or poor little Charmander's tail fire is submerged under a tidal wave of water. Or do they? We know for a fact that cloning is possible in the world of Pokémon; but do we know what the machine that your Pokéballs go into does? You can probably hear the jingle that plays in your head even now. Is that the sound of your dead Pokémon being cloned and handed back to you like nothing ever happened? This just got weird.
Related: what happens to the hordes of wild Pokémon you grind into the dust every time you EV train a level 80 Salamence? No one seems to care.
Where does it end?
If all the animals are Pokémon, and the bugs and fish are Pokémon, and even garbage bags and ghosts and levitating swords are Pokémon, are germs Pokémon too? Where does it end? Are you murdering a Pokémon when you swat a mosquito with the flat of your hand? When Nurse Joy administers vaccines, is she wiping out entire strains of Pokémon? Are people Pokémon too?