Are elgyem and beheeyem really from other worlds? What about cleffa or lunatone & solrock, and what about deoxys? Is this proof of extraterrestrial life? Could there be another world out there that evolved pokemon, and could it be habitable for us???

Of these, deoxys technically is from space but not from another world. It’s simply an extraterrestrial virus that mutated after exposure to certain types of radiation in space. (We know this via computer simulations and a digital analysis of samples taken from an inactive deoxys core.) Of course, the specific origins of said virus aren’t known, but it’s likely it simply came to be on the surface of an asteroid.

As for the others, that entirely depends on which theories you follow, as this is actually a matter of heated debate among scientists—particularly when it comes to the cleffa line. The most popular theory states that the elgyem line is indeed extraterrestrial in nature, as its appearance in Unova was abrupt and confined to one area.

Regarding cleffa, if it had indeed been extraterrestrial, it came here thousands if not millions of years ago, as clefairy colonies are well-established and often ancient (albeit extremely difficult to find). And lunatone and solrock are thought to either be sentient meteorites or mutated (and thus inactive) evolution stones, depending on whom you ask in the scientific community.

Personally, though, and in regards to your last question, I believe that even if these pokémon didn’t actually come from space (although I also admit that I believe they did), statistically speaking, there’s no doubt there are inhabitable worlds out there—and, perhaps, extraterrestrial pokémon. It simply wouldn’t make sense for there to be a great vastness that only developed one instance of life, to be frank.

How do genderless Pokemon reproduce?

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Re, the first question: carefully.

In all seriousness, these questions are actually more or less answered here: http://bills-pokedex.tumblr.com/post/153028583556/how-is-it-that-two-dittos-cannot-breed-two

To summarize, when in the presence of a ditto, the ditto takes on the form of the subject pokémon … only with appropriate reproductive organs. The ditto lays the egg (more often than naught), and the “genderless” pokémon (they’re actually in possession of male and female reproductive organs typically) fertilizes the egg. On their own, however, these “genderless” pokémon reproduce in a variety of ways, from fission to self-fertilization. 

The latter is true for solrock and lunatone … in a way. Rather than lay eggs themselves, as genderless pokémon cannot lay eggs, they spray nearby rocks with spores, which convert the stone into a baby solrock or lunatone that is genetically identical to the parent.

(You’re welcome for that mental image, by the by.)

Lunatone and Solrock

Lunatone
The Meteorite Pokémon
Type: Rock/Psychic
Official Registration #: 337
Entry: A cave-dwelling, moon-shaped meteor pokémon. Due to the fact that it had been discovered at the site of a meteoroid strike, popular theory states that lunatone came from space. Although there has been no definite evidence proving this, it’s very clear that lunatone is affected by celestial objects: as the moon gets closer to being full, lunatone begin to swarm and grow in power. On the night of the full moon, lunatone begin to glow intensely, and such a sight has been known to intimidate even the bravest humans and pokémon. Just about the only creatures who are not intimidated by lunatone in this state are members of the clefairy line, who have been known to mistake lunatone for the moon itself and proceed to engage in prayer dances beneath lunatone swarms to appease their lunar deities.

Solrock
The Meteorite Pokémon
Type: Rock/Psychic
Official Registration #: 338
Entry: A cave-dwelling, sun-shaped meteor pokémon. Due to the fact that it had been discovered at the site of a meteoroid strike, popular theory states that solrock came from space. Although there has been no definite evidence proving this, solrock are greatly affected by the state of the sun. During sunny days, solrock become more energetic and are capable of storing sunlight within its body. When it spins, solrock can release this energy in the form of intense waves of heat and light. As this is a cave-dwelling pokémon that has no known sleep cycle, this behavior has also been known to greatly confuse the clefairy it sometimes cohabits with.