With over 1,000 episodes under its belt and over 20 years on the air, the Pokemon anime has covered many mysteries in the Pokemon World, such as the Mega Evolution phenomenon, the origin of the Ultra Beasts, and, most recently, what Ash actually wants out of life after a couple of decades of just battling for the sake of it. That being said, not all mysteries in the series have been solved, with many being a one-time occurrence that is never talked about again.
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Some of these mysteries have persisted since the very first season of the anime, with the writers apparently forgetting that these events and storylines had ever happened, continuing on with the story, and leaving them as mysteries for the foreseeable future.
10 The Legendary Mural
After Ash has to rush Pikachu to the Pokemon Center following the pair being attacked by a flock of angry Spearow, Ash talks to Professor Oak while claiming that he saw a Ho-Oh, pointing to a carving of the monster on the wall that is accompanied by a handful of other legendary Pokemon. One Pokemon that definitely doesn't belong on this mural, however, is Arcanine, which isn't a legendary Pokemon. While it is the only Pokemon that is described as a Legendary Pokemon in the Pokedex, this doesn't explain what it's doing on an ancient carving next to Ho-Oh.
9 Crystal Onix
Early in the series, Ash and his companions encounter a strange Onix that is made of crystal rather than rock, being immune to Water-type attacks rather than being weak to them and living in an underground lake inside a cave. The origin of this Onix and the implications it has on the rest of the series are never touched upon again, and the Onix is never mentioned nor seen in any subsequent episodes, leaving most questions about the monster unanswered.
8 The Giant Dragonite
Although the episode Mystery at the Lighthouse is an adaptation of Ray Bradbury's novel The Fog Horn, which led to the creation of the Godzilla film series, it manages to force fans to question how such a massive Dragonite could survive without being seen for so long and how it grew to such an enormous size in the first place, as this isn't just a simple sea creature.
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Giant Pokemon have returned in the series multiple times, with the Dynamax mechanic in Sword & Shield and, most recently, Go's giant Magikarp in Pokemon Journeys, but the mystery of how this giant Dragonite came to be has never been touched on or mentioned again.
7 What Happened To Ash's Primeape
Ash's Primeape marked the progression of Ash's character growth as he began to actually work for his successes rather than waiting for someone to pity him, even if Ash didn't keep Primeape for too long. After entering the P1 fighting tournament and coming out victorious, Primeape was left with another trainer in order to get even stronger, but, like Butterfree, the audience has no idea what happened to them in the years since. It's expected that, due to Butterfree's short life span, Ash's Butterfree is now dead and his Pidgeot is waiting patiently outside Viridian Forest for Ash to return for it, but the status of Ash's Primeape is a larger mystery.
6 Caterpie's Evolutions
As the first Pokemon in the series to evolve, it should be no surprise that Ash's Caterpie's evolution methods were a little different from every evolution that came after it. Instead of transforming in bright, glowing light, Caterpie coats itself in its own String Shot to create a cocoon and turns into Metapod, then the cocoon cracks open after defending Ash from a Beedril to emerge as a Butterfree. While this makes sense in the real world, this kind of evolution is never used again and is never explained as to why it's so different, with one exception.
5 Slowpoke's Evolution
Like Ash's Caterpie's evolutions, the first time a Slowpoke is shown evolving on screen it "evolves" the ways its Pokedex entry says it should. After a Shelder bites its tail, the Slowpoke has enough weight on its rear end that it can stand on its hind legs and use its arms for punching moves. While this raises some questions on its own, since this means that there are Slowpoke that fish using their head rather than their tail, it's an evolution method that isn't shown all that often and it is never explained why Slowpoke's evolutions are so different.
4 Why Pokeballs Hurt Jesse
For the longest time, fans of Pokemon have wondered what actually happens to a Pokemon when it is captured inside a Pokeball and how a Pokeball actually works. While this question is never talked about nor answered, one particular scene raises even more questions when Jesse is accidentally hit by the beam of light that comes from a Pokeball and is apparently electrocuted.
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While this does seem to confirm that people can't be caught inside Pokeballs, despite the fact that Ash proved that trainers could catch inanimate objects inside them by catching a rice ball instead of Primeape, it leaves one major question as to what the beam of light does to a Pokemon that is so painful when it hits a human instead.
3 Professor Oak's Partner Pokemon
In both the anime and video game series, Professor Oak is an ex-Pokemon trainer turned Pokemon researcher who grants new trainers their first Pokemon, as well as exploring the many mysteries of the Pokemon world. One mystery about him that is never explained is who his partner Pokemon was while he was a trainer. When Ash traveled back in time thanks to Celebi's shenanigans and met a young Professor Oak, he had a Charmeleon in his possession which may indicate he has either a Charmeleon or Charizard somewhere in his lab, but this Pokemon is never seen and the audience never finds out what happened to it.
2 Ash's Lackluster Trainer Skills In Unova
The Unova anime and games acted as something of a soft reboot of the series, with many Pokemon in the Unova region sharing similar design characteristics to those found in Kanto, though one of the biggest mysteries surrounding the anime has still been left unanswered. After his meteoric growth in the Hoenn and Sinnoh regions, Ash travels to Unova and subsequently forgets everything he has learned since he left home, then suddenly remembers how to be a good trainer when he arrives in the next region, Kalos. This could just come down to bad writing choices, but why he suddenly took a turn for the worse is never explained nor expanded upon in subsequent seasons.
1 Who Ash's Father Is
The biggest mystery in Pokemon and the source of many fan theories is the identity of Ash's father. In the first few episodes, it is revealed that both Ash's father and grandfather left on a Pokemon journey, but neither of them returned home at any point in the series. Some fans think that Giovanni, the leader of Team Rocket, may be Ash's father, though this was before it was revealed that the rival of the Johto region, Silver, was actually Giovanni's son. Unless the two are brothers, this seems like an unlikely conclusion and leaves the mystery entirely unsolved.