Due to all the fascinating people and places in the Pokemon world, it makes sense that many would be too preoccupied with collecting badges and completing their pokedex to be overly concerned with what lies outside this world. However, in one's journeys, it is likely that certain peculiar pokedex entries have caught one's eye.
There are quite a few entries about pokemon species with mysterious and unknown pasts that may not have come from the planet. Those tied to the sun, moon, and stars can be found more commonly than most expect. Some have even theorized that all pokemon are from outer space, though there is nothing that definitively confirms (or denies) this fan theory. Although, with the number of indications that can be uncovered, it is clear that at least a few pocket monsters have extraterrestrial origins.
10 Deoxys
As one of the most alien-looking pokemon, Deoxys is the legendary that comes to mind when most think about pokemon that come from outer space. With a very bizarre body plan indicating biology unlike anything found in the world, this immensely powerful Psychic-type can perform some astonishing feats, like regenerating entire limbs. Another trait that should be noted is the gem in its chest that glows when it tries to communicate or attack. Flashing lights in these manners are often linked to pokemon with extraterrestrial origins.
The majority of its pokedex entries mention that Deoxys is some sort of off-world virus that mutated into a pokemon. Its entry in Pokemon Ruby for the Game Boy Advance mentioned that it mutated due to coming into contact with a laser beam, though does not state what produced this beam of energy to begin with. There are more questions about this pokemon's origin than any other because of how scarce the information about it is before it came to the pokemon world.
9 Rayquaza
Many consider this serpentine Dragon and Flying-type pokemon to be the guardian of the skies and a part of the world's natural ecosystem, however, it holds some enigmatic qualities for a being that's meant to be linked to the planet. It is part of the Weather Trio consisting of Kyogre, Groudon, and themselves as the Trio Master. They are known to quell battles between the other two members of this trio in order to maintain balance. Unusual, given the series' format of often making the leaders of trios preside over the group from without, like how Lugia is the trio master of the legendary birds Articuno, Zapdos, and Moltres.
However, the sky encompasses the land and sea, separating it from outer space. Rayquaza is seen in the anime, and sometimes other media, being able to travel beyond the world's atmosphere completely unhindered. Being able to not suffocate in space and having the power to dominate other legendary pokemon similar in power to themselves potentially points to Rayquaza originating off-world.
8 Elgyem & Beheeyem
Elgyem, the large-headed Psychic-type, and its evolution are clearly references to the Roswell, New Mexico UFO sighting that occurred in 1947. Many of their pokedex entries mention that Elgyem is a species that was completely unheard of until they were found in a desert, apparently linked to the crash site of a spaceship.
Beheeyem's entries often mention that it using the colored dots on their hands to create flashing signals in order to communicate. With this ability, it is said to be able to alter another's memories. Although mind manipulation is not an uncommon trait for a Psychic-type, very few are mentioned to mess with someone's memories. This is likely a reference to what aliens apparently do to humans in numerous cases where people have reported being abducted and experimented on by extraterrestrials.
7 Lunatone & Solrock
These two dual-type Rock and Psychic pokemon look very much like celestial objects, which is the clearest indication of their origin. Proof of their past can be found in the location from the Generation III games where they can be encountered and captured: Meteor Falls.
Much of their pokedex entries mention that their sightings coincide with meteors crashing into the planet. Furthermore, their activities are seemingly linked to the celestial bodies to which they bear resemblance to. Lunatone becomes far more energetic when the moon is out and Solrock is the same when the sunlight is strong. This may be an indication that the meteors that brought these species to the pokemon world were connected to, or passed by, the sun and moon.
6 Cleffa, Clefairy, & Clefable
These cute, Fairy-type pokemon are one of the first evolutionary lines in the franchise to have a link to outer space. Cleffa is often referred to as a star-shaped pokemon and many of its pokedex entries mention that sightings of this usually rare pokemon significantly increases around times of meteor impacts, not unlike Lunatone and Solrock.
When evolved after acquiring enough happiness from spending time with their trainer, Cleffa becomes Clefairy, a pokemon whose powers are linked to the moon and is sometimes known to be so full of power that on some nights its tiny wings gain enough energy to let it fly. Their connection to the aptly named Mt. Moon in the Generation I games makes it clear that this species is deeply connected to the eponymous pale celestial body. Furthermore, the only way that they can evolve into their final form, Clefable, is by using a Moon Stone; objects imbued with a mysterious energy that are possibly shards of meteorites.
5 Kyurem
Here's another Dragon-type, this time also part Ice, that stands out a bit among legendary pokemon. Kyurem, like Rayquaza, is a Trio Master that resides within the trio they rule alongside Reshiram and Zekrom. However, things are a bit different, as countless bits of in-game information imply that the three Dragon-types were once a single being.
The Tao Trio of the Unova region was not only said to be from a single form but also to have arrived at the pokemon world via a comet. Different from meteors that are mostly rock and metal, comets can be composed primarily of ice, making one an ideal vehicle for the original tao dragon to travel with.
4 Eternatus
As a being that looks more like a Persona 5 summon than a pokemon, it is understandably an entity from off-world. Eternatus, the gigantic Poison and Dragon-type pokemon, was said to be sleeping within a meteorite for 20,000 years. With a skeletal frame and almost no features that make them seem like part of the world's natural ecosystem, its appearance is almost difficult to parse when first seen by many players.
Their colossal size and tremendous power also indicate that it could not have possibly originated among other terrestrial pokemon, or even on another planet. It can be argued that a form that is a ridiculous 65 feet long with no means to eat (in a traditional sense) can only be the traits of a creature that originated in the void of space. Its pokedex entry from Pokemon Sword says that it lives off of the energy that it absorbs from the entire Galar region through its glowing core — a core that is eerily familiar to that of Deoxys and a couple of other space-linked pokemon.
3 Minior
With two separate forms that shift depending on how much HP this Rock and Flying-type pokemon has, Minior can be classified as the definitive "meteor pokemon." Their hard-shelled defensive Meteor Form looks very much like a stone that can survive traveling through space while their Core Form resembles an energetic, newborn star. From the pokedex entry that can be read in Pokemon Moon, players can learn that this twinkling little star is actually made from mutated nanoparticles in the upper atmosphere.
The entry from Pokemon Sun elaborates on its unique ecology by mentioning that Miniors feed upon dust in the air, a strange food source, though not an unreasonable one due to their Rock-typing. Even more interestingly, however, the entry from Ultra Sun states that this species lives in the ozone layer of the planet and is often food for stronger pokemon. It is not mentioned what kind of high-flying pokemon feed on rock-like organisms, nor is this fact ever addressed again, leading some to believe that there is more going on in the upper atmosphere of the world than more realize.
2 Staryu & Starmie
Although clearly based on starfish, there are elements of this line's biology that point to it not originating in the seas of the world like how some think. Many pokedex entries from across the series say that Staryu usually resides on the seafloor, though rise to the surface at night to engage with the stars twinkling after dusk.
Their central gems glow brightly when doing so, much like when attacking, indicating that this may be communication, though there has yet to be a definitive explanation for this odd behavior. When weakened, their gems will slowly blink to show this. If one ever loses a limb, they can regenerate, which in combination with their flashing light communication method parallels qualities held by other confirmed space pokemon like the Elgyem line and Deoxys. There's simply too much of a pattern for Staryu and Starmie's origins to be anything but extraterrestrial.
1 Igglybuff, Jigglypuff, & Wigglytuff
This line of pink pokemon that are both Normal and Fairy-type don't seem alien at first glance, though when one considers some of their unique qualities, as well as contextual information from events, the theory of them being from outer space will not seem that strange. Firstly, take note of the natural lift that both Igglybuff and Jigglypuff get while traveling. They can float, and sometimes fly, without any wings or special powers. They're so light that they can do this naturally as if they originated on a planet with lower gravity.
Next, consider that Jigglypuff needs a Moon Stone to evolve. Needing spaceborne energy to reach their final form is another indication that this line is more alien than they seem. In Pokemon Go, during Enigma Week, Jigglypuffs could be found and caught among many other pokemon tied to outer space, which is incredibly suspect when considering their origins. Finally, in their first appearance in the games during Generation I, they can mostly be found around the area most dedicated to outer space: Mt. Moon.