I absolutely love that the Pokémon universe is literally tearing itself apart at the seams. Fantastic worldbuilding, A+++
ALTALT
A non-exhaustive list:
Mega Evolution comes from a meteor. The impact of that meteor literally split the dimensions apart and made it canonical that different versions of the same game are parallel dimensions (Alpha Ruby is a different world from Ruby, for instance). This is later confirmed by the presence of Anabel in Sun and Moon, who fell through dimensions from a world without Mega Evolution.
Speaking of Sun and Moon, wormholes are opening up all over Alola, letting in extradimensional beings that Pokéballs don’t catch properly. There are silver-skinned humans from one of these portals that live in a giant prismatic city.
Also in Sun/Moon, you can pass through to a mirror world where day is night and night is day. When this happens, you can catch the mirror world version of your box legendary friend.
There’s a giant space alien in Sword and Shield who’s leaking particles that cause Pokémon to briefly turn massive, which sometimes rearranges their genetic makeup.
In Scarlet and Violet, reality is splintering. There’s a hole to the future/past that generates paradox Pokémon which are heavily implied to have been materialized out of a researcher’s desire to see them rather than actually from their future/past. The same energy that supposedly made them enables Pokémon to become any type they want and caused a robot to gain human sentience.
In the hole you find the paradox Pokémon in, you find buried monoliths that nobody knows where they came from. The very material they’re made of is canonically unidentifiable.
Time and space were briefly unraveled in Pokémon Diamond/Pearl/Platinum as a maniac tried to overwrite the current world and make a new universe out of it, and in the Platinum universe, this opened a hole to another dimension where a banished god lives. The banished god was pissed off about this and abducted the guy that messed with time and space.
People sometimes slip through the cracks and become Pokémon in Pokémon-only worlds (the Mystery Dungeon series) or drop through time to different eras (Legends Arceus’s protagonist and Ingo).
In Mystery Dungeon, time is eroding (Explorers of Time/Darkness/Sky), and the world is warping and distorting into areas that scramble themselves every time you enter them and make the inhabitants of those areas agitated and hostile (entire series).