Summary
ThePokémonworld is full of countless adorable and terrifying creatures. The worldbuilding shows a planet that has become one with nature as both Pokémon and people live side by side. Some will live a quiet life while others seek to become stronger by challenging others, building new teams, and exploring every corner of the world.
There is plenty to see and explore but also deep-rooted mysteries that no amount of traveling will give you an explanation for. From vanishing phantasms to questions about historical events, these are the ten greatest Pokémon mysteries that have not been answered yet.

10What Is Under A Diglett?
Missing Feet
One of the longest-standing Mysteries of the Pokémon universe revolves around the rock ground-type, Diglett. Diglett is known for burrowing underground like a mole and evolving into Dugtrio, but there is one detail that has never been seen before.
Neither Pokémon has ever had their feet fully shown with every key art, instead, showing the dirt around their lower half. Even when picked up in the anime, Diglett is shown to keep his rock base, so what could Diglett’s feet look like?

9What Happened In Pokémon Legends?
Lost Time Travelers
Pokémon Legends Arceus brought back the Protagonist from Diamond and Pearl and it also brought in Ingo from the Black and White series. These characters were thrown back in time into feudal Sinnoh with no foreseeable way of returning to their original periods.
In the story, the main character must complete the first Pokédex, help establish human relationships with Pokemon, and reveal the deities of the world as two separate entities. After everything is completed, you expect your character to find a way home, but none of the characters who were sent back are seen going home.

8Who Was The Ghost Girl?
X And Y’s Biggest Mystery
The 6th generation of Pokémon weaved a tightly-knit story that extended into the remakes of Ruby and Sapphire. One storyline that spooked players and never got explained was the mysterious ghost girl.
Taking the form of a Hex Maniac, her most notable quote is “No You’re Not The One”, before vanishing. If you aren’t the one, then who is? Ghost Girl would also appear again in Omega Ruby and Alpha Sapphire on Mt. Pyre, where she seemed to be building up to something, though what it could be remains unsolved.

7What Were The Pokemon Wars?
Lt. Surge’s Backstory
One of the best-known Pokémon Wars was the war between Kalos and an unknown region. There is also evidence of other wars occurring throughout history. However, not all wars took place in the ancient past.
In the original Pokémon games, Lt. Surge is known for havingparticipated in at least one war in his lifetime. The specifics are never looked into too deeply, so there is no record as to which regions could have been fighting or for what purpose.

6What Does Cubone Look Like?
Pokemon’s Saddest Story
Cubone is always depicted as being a sad little creature who lost its mother, and the skull on its head is said to be the same bones from a mother Marowak. However, this begs the question; if Cubones are born from eggs, why are they automatically born with their iconic bone helmets?
Another mystery is the true face of Cubone, sand since the skull is not attached and can be turned around like a real helmet, therefore it is definitely possible to remove it. The franchise has never revealed what’s underneath.

5How Are Eggs Made?
Eggs Are Not Laid
How are baby Pokémon made? First, you need to find two compatible Pokémon and leave them in the daycare, then you walk around for a bit and suddenly the caretaker will find aPokémon egg. While it may seem obvious that the parent Pokemon produced it, evidence in Sinnoh suggests otherwise.
A little girl in Solace town will claim that no one has seen a Pokémon lay an egg, and even Caretakers will also be surprised to find an egg but never be around to see it get lain. Perhaps Arceus is responsible due to its ability to create legendary eggs out of nothing, but the actual process remains a mystery.

4Who is Ash’s Dad?
The Usual Suspects
The Pokémon anime has a few mysteries that have never really been unraveled, and the most notable is the identity of Ash Ketchum’s father. However, there was a non-canon stage play that revealed it to be Giovani himself.
Ash’s father is seldom mentioned in the Anime; even with Ash’s final appearances as the protagonist, the topic is only ever touched in the adventures of Ash from the film continuity. Even then, no official identity or even reason for never coming back is revealed; instead, Professor Oak often takes on a paternal role for the Pokémon World Champion.

3What Were The Legendary Beasts?
Raikou, Entei, And Suicune Origins
The Paldea region’s DLC introduced brand-newparadox formsto the legendary beast Pokémon, and these prehistoric blends were odd but made sense in the greater context of the story. However, had they truly been prehistoric versions of the legendary beasts, it would have been a huge 180 from one of the most mysterious legends of the Johto region.
When three unknown Pokémon were killed in a fire, they would all be brought back to life through the power of Ho-oh as the mythical beasts. The identity of these original Pokémon is yet to be explored.

2How Do Pokeballs Work?
The Nature Of Pokeballs
Pokeballs were created to allow trainers to capture Pokémon and keep them as allies. While the functional use of Pokeballs is known to all, there are still some questions as to what they are capable of or even what it’s like for a Pokémon to be inside one.
Some Pokeballs, like the luxury ball, are known to be extra comfortable for the Pokemon inside though the specifics are unknown. It is also unknown if a Pokeball will work on a human, but it has been known to capture inanimate objects such as rice balls.

1Which Region Did Kalos Fight?
The Ultimate Weapon
One of the biggest mysteries of the Pokémon world was presented in Pokémon X and Y. Thousands of years ago, a war was fought between Kalos and an unknown region, and to win the war, Kalos fired their ultimate weapon across the globe.
It was originally believed that Galar was the region devastated by the weapon, but later theories cropped up about Paldea’s crater being the ground zero of the weapon’s impact. Despite this, there has been no official confirmation to explain where it actually hit or even the original region that was involved in the conflict.