The enduring mystery of where Pokémon come from has lead to many theories over the years. It's well known that some Pokémon, like Mewtwo, are man-made, others are born naturally and more still come from objects. They're definitely not animals, as there are mentions of real animals in the Pokémon anime, though they are never seen. So what are Pokémon? One popular theory is that Pokémon are actually aliens. Although it sounds crazy, that theory has actually been hinted at multiple times across the Pokémon franchise.
The first exploration of this theory comes from the original Pokémon: Indigo League series. In Season 1 episode 6 of the anime, Ash, Misty and Brock encounter an eccentric Pokémon researcher named Professor Seymour on a hike to Mt. Moon. Seymour explains his theory that Pokémon, most specifically Clefairy, actually come from space. His theory is backed by the fact that Clefairy rely on the properties of the mysterious Moon Stone to evolve. In the anime, Moon Stones are actually fragments of crashed meteorites that have been scattered across the Earth. A particularly big one is on Mt. Moon, where a herd of Clefairy live. Seymour claims that the Moon Stone on Mt. Moon is actually the spaceship the Clefairy used to travel to Earth.
This idea that Clefairy are actually aliens is further explored in Pokémon Season 1, Episode 62, Clefairy Fables. In it, a bunch of missing items have been stolen by Clefairies. Ash and friends encounter another professor, Professor Oswald, who theorizes that the Clefairy are stealing these items to recreate their spaceship and return to their home planet.
This theory turns out to be true, at least in the anime. But what about all the other Pokémon? Do all 806 other Pokémon originate from space? The games provide some substantial clues.
Gen 4 introduced Arceus, the god of Pokémon and apparent creator of the universe. If the myth holds true, then Arceus technically counts as extraterrestrial. Gen 4 also introduced Pokémon Dialga and Palkia, rulers of time and space, respectively. Both Dialga and Palkia were created by Arceus, so these Pokémon might also count as aliens, as well as Giratina, Arceus' renegade creation, controller of antimatter and sole inhabitant of the Distortion World - a dimension completely out of time and space
Though whether Arceus, Palkia, Dialga and Giratina are aliens is debatable, since Gen 3 there's been at least one undisputed Poké-alien -- Deoxys. Deoxys is undoubtedly, 100% an alien, as it was formed through the mutation of a virus in outer space. It arrived on Earth inside a meteor, just like Clefairy. There's also Gen 1's Staryu and Starmie, who communicate with "something beyond the stars" at night, Gen 3's Solrock and Lunatone, the living meteors, Gen 5's Elgyem, whose appearance is linked to a UFO crash site, Gen 7 legendaries Solgaleo, Lunala, Necrozma and the Ultra Beasts, all of whom come from a different dimension and Gen 8's Eternatus, who came from a fallen meteor.
A surprisingly large variety of Pokémon come from outer space, with a few being introduced each Generation. From Arceus, the creator of all, to the gigantism-inducing, apocalypse-causing Eternatus. With such a variety of unique and influential Pokémon coming from the final frontier, the idea that all Pokémon could be extraterrestrial certainly has some credence. And, though nothing is certain, it's a definite fact that plenty of Pokémon come from or can survive in space; in other words, the idea that Pokemon are aliens might not be so far-fetched after all.