Pokémon/WMG/Open Two

General Wild Mass Guessing for the Pokémon franchise. This includes theories that span multiple generations and multiple Canon.

NOTE: To prevent Archive Panic, all new Guesses are to be put on Page Three. Responses to theories on this page are still welcome.

The 100 or so new Pokemon in each generation are part of a vast conspiracy.
Every time somebody says something limiting the number of Pokemon, it's true. Professor Oak really did say, three years before G/S/C, that there were only 150 Pokemon, and every time someone mentions a Pokemon from more than three years ago that wasn't around during the first generation, they're lying. Celebi is in on it too, the 4th movie was just an illusion to make things more realistic, as were most of the later movies (Heroes and Jirachi Wishmaker especially). The source of the Pokemon is that each "generation" is a literal generation of 'Pokemon, and because of their metamorphoses described as evolution'', they have sudden surges of new breeds appearing and old breeds gaining or losing abilities every couple of years. Pikachu is not really a Pikachu, but rather an entirely new Pokemon akin to Mew or another legendary, which Professor Oak sent along with the trainer who was to be the focus of the conspiracy. (All of Team Rocket from Johto onward are in on it, with the exception of Jessie, James, Butch, and Cassidy.)

Alternatively, the universe undergoes constant renewal.
Why do they never mention another generation? Simple, because each generation is its own universe. Each reality collapses on itself via Big Crunch, and is reborn as the next generation. This is why Ash is forever 10-because each season's Ash isn't the same as before. That, or Arceus causes a Cosmic Retcon every once and a while for shits and giggles.

Poketopia is run by Cipher.
The entirety of Poketopia (in Pokemon Battle Revolution) is a ploy for Cipher to regain power after Pokemon XD by building up cash and Pokemon reserves through legitimate business. This would make Mysterial either Greevil's superior or someone who stepped in to fill the power void left by Greevil at the end of XD. Sashay may be a high-ranked officer - maybe even an Admin - due to her being the only trainer who has the Cipher riff used in Colosseum and XD in her battle theme.
 * Adding on that, Joe is Mirakle B.'s civilian self and he will defect to team Miror B. as soon as he learns of its existence. Kruger is Cipher's new enforcer, taking the position from Dakim. He was a former leader of a "normal" family which got assimilated by/allied with Cipher (The "Kruger Family" trainer class aren't his relatives, their his underlings)
 * Or it's a splinter group of Team Cipher. Specifically those that have the ambition of Team Cipher, but not the lack of a moral code. They were booted out because Team Cipher hates morality in itself.

What we know as evolution is actually a metamorphosis, thus: actual Pokémon evolution happens over time just like in the real world
If we take into account that the Pokémon world is a product of an apocalypse Pokémon are descendants of animals living today through mutation/adaptation/evolution. The first Pokémon produced were the ones that we find as fossils in the games. These Pokémon are said to have died out, but perhaps they simply evolved themselves. It wouldn't be a far stretch to assume that the Scyther family evolved from Kabutops. The Omastar lost their shells and became Tentacool or moved to a hotter climate and became Slugma. Shieldon became Aron. More suggestions welcome.
 * Hmmm... The Pokédex Extended Fanon Edition sounds like it could fit in here.
 * Lileep must be Sudowoodo.
 * This Troper tried to compile a list of Pokémon that look alike and should be related. Find it here. It is, obviously, incomplete.
 * The Caterpie, Weedle and Wurmple lines share a common ancestor. Furthermore, Wurmple is starting to diverge into two different kinds of Pokemon as well - Dustox and Beautifly.
 * Gligar/Gliscor and Skorupi/Drapion may have some kind of connection. There's also Gligar/Gliscor and Zubat/Golbat/Crobat.
 * Nidoking/Nidoqueen and Rhydon and their evolutionary families are very closely related. Lapras may also be related to them Nidos.
 * Remember, Magikarp used to be waaaay stronger in the past. Evidence of evolution!
 * Look at this.

Pokémon are the groundskeeper species of Earth, placed there to prevent humans from ruining the place and keeping them occupied.
There is another species, possibly still in charge and possibly Pokemon themselves, perhaps Unown. The Pokemon are there to filter out pollution (Grimer, Muk, Koffing and Weezing) and make them gross but harmless compounds, take care of, pollinate, and plant plants (bug and plant Pokemon), keep the oceans clean and rescue people from drowning (Water Pokemon), and protect people from the elements and balance the effects of other Pokemon (ice, fire, electricity, etc), as well as provide less-pollutive sources of power. The Dark and Steel Pokemon types were added to balance Psychic helper Pokemon and be more durable for menial labor such as cut and rock smash.

All grass and trees are sentient species of Pokémon.
They just can't do anything that humans can notice. Also explains why small trees and patches of tall grass grow back when you cut them.
 * So, can we expect something like The Happening?

Ten years old in Pokemon is the equivalent of fourteen in Real Life (and that's a low estimate)
It really stretches Willing Suspension of Disbelief to think about ten-year-olds going out unsupervised training wild monsters, especially when they have powers over Earth, Fire, Wind, Water, you know. It makes slightly more sense if you think of said 10-year-olds as teenagers, so while they're still idiots, they are at least biologically mature (however that helps). It's not like any canonically age ten characters actually look that age anyways. For the record, why choose fourteen? That's the minimum age you can get a Learner's Permit in Canada (you technically still have to be supervised, hence the "low estimate").
 * Actually, as a Canadian, I can tell you that in almost every province, the minimum age is 16. Looks like Pokemon ten year olds are even more mature than we thought.
 * That would explain why May and Max look 14 and 10 instead of 10 and 6. And Ash's appearance would change less over a given period of time the older he was... You may be onto something, which brings up an interesting crossover WMG with world that uses weird physics and probably a longer year than normal.
 * This could be explained by having the Pokemon world nearer to its sun than Earth, mean the years would be shorter.
 * No, for this we need the years on the Pokemon world to be longer than our Earth's years, and the Pokemon world needs to be farther away from the sun then our planet. If the Pokemon world was closer to their sun then Earth is to ours, then when someone on the Pokemon world was ten, they would have a lower age measurement number here, as their year would take less time then our Earth's years.
 * While a longer year explains Ash's effective unaging immortality, it's not strictly necessary. Remember, we're talking ten-year-olds in a universe where a CD can be used to teach a dog/fox hybrid to change the weather, and where the average trainer has the equivalent to six walking, intensely loyal, (kinda) talking weapons of mass destruction following him or her at all times. And even empty poke balls act like ranged and highly effective stunguns when used against humans. Even if the trainers haven't reached the age of maturity, they should be of equal intelligence to many high school students in the real world, and more than well enough equipped to defend themselves or deal with emergencies. Ash is... special.
 * Here's one for ya - the humans of the Pokemon world are not, technically, the same species as the humans of our world - their genome is similar enough to put them in the same genus, but they aren't our humans. The Poke-world human grows to physical and mental maturity faster than we do, the same way that some animals are independent just days after birth and others stay with their parents for years.

Legendary Pokémon (especially Arceus) are nowhere near as powerful as they are claimed to be. They are just extremely powerful animals that seem to correlate with well known Myths.
This would explain why there are demonstratively multiple copies of supposedly one-of-a-kind Pokemon, why dimensional warping beings can be controlled by 10 year olds, and why a common Wobbuffet can defeat the creator of the universe.
 * Alternatively, the ancestors of today's humans saw how powerful they were and came up with stories about them. Dialga can control time to an extent, so early humans came up with the myth that he created time, etc. Arceus was pegged as the creator of the universe because of its incredible power and divine appearance. See African and Native American folklore involving animals for a real-life equivalent. In the Mystery Dungeon games, the legendaries are either deliberately deceiving the other Pokemon (who have also been exposed to the myths by hanging out with humans for so long), or have bought into those myths themselves.
 * Thank you SO MUCH for posting this theory. The general fandom's insistence that All Myths Are True has bugged me for ages, especially since you get to catch these Pokemon in-game and there's nothing that claims that the mythology is anything but.
 * Heck, just look at the legendaries themselves. We have a Creator God (Arceus), a Common Ancestor (Mew) and Alien DNA (Deoxys). They can't all be what they are reputed to be.
 * Well, they actually could, but only if you don't believe that creationism, evolution, and aliens are mutually exclusive.
 * This troper would like to add to this theory, as it makes the most sense. Consider, for instance, Kyogre and Groudon. Many view these two legendaries as the point where legendary Pokemon started becoming obscenely powerful, as those two in particular are credited with creating oceans and continents. Makes them sound like physical gods, no? But let's consider what we've seen these two do. Kyogre can make it rain endlessly, Groudon causes a drought. Endless rain could create oceans easily and endless, intense sun could dry up oceans to create continents. It's easy to see how, from those particular abilities, one might be convinced that they're responsible for shaping the Earth, when in reality all they can actually do is manipulate the weather. This is something just about every Pokemon can already do, just not to the same extent as Kyogre and Groudon. So, when you think about it, while Groudon and Kyogre are special in having such abilities, they're not uberly powerful god Pokemon.
 * This troper has an alternate theory regarding the origin of Legendary Pokemon. In this troper's opinion, today's legendaries are the remnants of ancient extinct species of Pokemon. Eventually, as the rest of their species died out, one or two of certain kinds proved resistant and survived, and underwent a special "Ultimate Evolution", which gave them a more majestic, legendary appearance, greater power, immortality, and in many cases, loss of gender and/or sterility. Eventually, over time, humanity formed myths about these Pokemon, and we get to where we are today. There is support for this theory, such as why some legendaries still have genders, and why you can breed Manaphy to get Phione, but the Phione won't evolve into a Manaphy. The Phione is the species that Manaphy used to be, but it underwent the one-of-a kind evolution and became what it is now.

It's also worth mentioning that, if Palkia and Dialga really were rulers of space and time, then destroying the world would have been a trivial matter. Dialga could stop time and destroy the world at its leisure, Palkia could likely just make it disappear, and the two working in tandem could do this while time is stopped so no one else could interfere. Either way, using their specific powers to try to destroy the world likely wouldn't have caused the sky to go funny. The legends regarding their particular abilities could, instead, relate to their signature attacks. If Dialga used Roar of Time and time seemed to stop/slow down while it was being used, then an onlooker might think it had control over time. Likewise with Palkia's Spacial Rend. And the legend regarding Arceus using 1000 hands to create the universe could stem from its Judgement attack, which apparently works by firing a lot of lasers at the target. And if Arceus was known to have created Dialga and Palkia, and Dialga and Palkia were assumed to be rulers of time and space, then it wouldn't be a stretch to assume Arceus is the creator of the universe. In fact, in the upcoming Heart Gold and Soul Silver games, Arceus seems to be able to make one of these Pokemon for the player while in some ruins. This suggests that Arceus does indeed have the power to create these Pokemon (under certain circumstances, mind you,) so someone who knew this and knew about Dialga and Palkia's powers could, as stated, think Arceus to be the creator. As such, all of them end up with their real capabilities being blown out of proportion in myths and legends.
 * Then how was it that Cyrus was able to creature miniature galaxies with them?
 * This idea is supported in Platinum. Cynthia said exactly the same thing about Roar of Time and Spacial Rend.
 * Perhaps they're the genuine article, yet everything else is a lie.
 * What could explain Reshiram and Zekrom's myth (the two of them originally being one dragon belonging to twin brothers that split when the brothers began fighting, each siding with a different brother, with Kyurem presumably being the remains of this dragon)?
 * An alternative idea I am positing in my fanfic Doom-Kindred (the main character of which "has" a Rayquaza and encounters a Deoxys) is that the legendaries are either mere splinters of the real thing (the physical gods etc) that have been trusted to what said gods see as a worthy individual or just incredibly rare and/or powerful Pokemon, but could still be feasibly one of many (Deoxys, Mewtwo, Latias/os and Lugia are clearly shown in various films or Pokedex entries to either definitely be part of a species or easily replicable). This also justifies obvious size, weight and power discrepencies; that 23' serpent is NOT the god which could be seen as the entire sky and atmosphere, but rather a very small fraction of its power made manifest and controllable for a teenager. Additionally, being created for a specific individual explains why the god-variant legendaries still understand human commands and nuances; the god has given the Pokemon created in its image all the necessary mental software to be 'a Pokemon'.

Alternatively, Giratina is the ONLY true Pokemon God shown so far.
Like it says above, Dialga, Palkia, and Arceus aren't Gods; Arceus created the first two and is extremely powerful, and Dialga and Palkia simply have the ability to control time and space, respectively, to an extent. However, the idea that Arceus created Giratina as well is also a myth; people simply related its powers to that of Dialga and Palkia, and thought that it was the same. And in Platinum, it was given the background that it was made to balance out the strength of the other two. But, think about what it did; when it appeared to stop Cyrus, it simply just... swallowed everything. Either doing that consumed all of its power, or else there would be a bigger battle between Giratina and the users of time and space. It's not too far-fetched to believe that it was an extremely powerful action, as we never saw where Dialga and Palkia went off to. In the end, the only reason it allowed you to capture it was because it trusted your character. And as the Poke Ball line acts as limiters, its true strength would never be used.

Also, compare their themes for a moment: Dialga and Palkia's, while odd, are more realistic and share themes with previous music. Arceus's, while... strange, is nothing too foreign. However, Giratina's is other-wordly, inhuman, and something from an Industrial artist's wet dreams (for the most part). Not just fitting as a being of anti-matter, but as a God. We might not know yet how Giratina came into being, but seeing as how it is in control of an entire mirror realm, and can stop things on ours whenever it gets too serious... it has the build of what seems to be the only deity faced in the series so far, not just some overhyped myth.
 * Hmmmmm... Personally I don't like that last part for several reasons. The most important being: Surely a god (especially since this seems to be meant in the sense of being intrinsically linked to the universe in question) wouldn't be "otherworldly" and would indeed seem as comfortable and in-place as is conceivable? It's like designing and creating a building where you would just feel... Wrong. Of course there's also a whole argument about anti-matter also not being all that different (the difference between matter and anti-matter is roughly analogous to the difference between positively and negatively charged things, so basically there's no difference until the two mix), but that's mostly an issue with the games themselves and can be easily excused because, well, it's Pokémon, we don't need realistic physics.

Legendary Pokemon marked as genderless do, in fact, have genders.
It's just that humans can't tell, either due to obscure ways of telling or not being able to get close enough to check. Fellow Pokemon can simply ask, which is why we see a female Celebi among other gendered Legendaries in Mystery Dungeon 2.
 * I remember reading in an official guide that it's not supposed to be "Genderless" but "Indeterminate Gender." So Pokémon like Magneton and Metagross can't breed with each other because you just stuck two Pokémon of the same sex together without realizing, because you couldn't tell! Ditto, being somehow able to copy DNA, can obviously tell what sex an "Indeterminate Gender" Pokémon is, and can therefore breed.
 * But that means that you would get an egg if, by pure chance, you happened to stick two Pokemon of the opposite gender together. Unless they don't breed well in captivity anyways, that is.

Pokemon don't have sex the way real life animals do.
They use what we would consider to be G-Rated Sex and magically generate eggs using some sort of ritual. This would explain how Improbable Species Compatibility is possible, why Pokemon genitals are apparently non-existent, and why no one has ever seen Pokemon lay eggs or presumably mate (they actually don't). Egg groups simply denote which Pokemon are capable of performing whatever ritual they use with each other. Legendaries can't perform the ritual at all, and dittos are capable of bypassing barriers altogether.
 * Magic? This can be explained with science. Pokémon are oviparous, and females will normally lay eggs, which are then fertilized externally by the males. Unfertilized Pokémon eggs bear almost no resemblance to fertilized ones (which can't really be explained by science), which would explain both why the egg-laying process has never been seen and why the child inherits so much of its move data from its father—the egg isn't really a "Pokémon egg", per se, until the father fertilizes it. (Maybe unfertilized Pokémon eggs are extremely small, similar to human ova.) The idea that the females lay the eggs regardless also explains why the only requirement of the instant egg cheat is the presence of at least one female that could normally produce an egg. The other parent could be a male of a different egg group, a genderless or legendary Pokémon, another female, or even non-existent, but if there is no female or the only female would normally be unable to be a parent, the resulting egg produces a Game Breaking Glitch.
 * That... that actually makes more sense than what I posted. Ladies and gentlemen, I think we have the answer!
 * Another idea is that Pokemon reproduce via pollination.

Oak/Elm/Birch/Rowan is putting in information in the Pokedex as a manufactured reward
You really are helping out the professor with his Pokemon research, but the result of said research will take years or more to come to fruition. Since the professor has underestimated your patience as well as intelligence, he puts in little bits of trivia into your Pokedex as a reward for catching Pokemon, in the hopes that you'll think that you're responsible for that new information coming to light. Unfortunately, he doesn't screen that information very well, resulting in things like the Raticate whiskers fiasco.

Another Version of the Pokémon World is a Product of the Apocalypse
The humans that came first were more war crazed than us (as in Real Life us). They blew themselves and most plants and animals up, but the survivors were saved by Arceus n' pals after they came from space. Uxie erased their memories, Mesprit made them more loving, and Azelf gave them more will to live. Giratina set up an underworld, Dialga and Palkia saved space-time from collapsing. Mew created the rest of the legendaries who messed with the land masses a bit, breathed new life into the place, etc. It then created a few normal Pokémon. Arceus n' pals really only did this because Mew felt bad for the humans. Over time, this got distorted into the myths we know now.

"Nurse Joy" and "Officer Jenny" are titles.
Both police officer and public medical expert are, if not government positions than at least established by a large organization (possibly the League). In this case, the job description explicitly requires them to interact especially well with pre-teens and young teenagers, and intelligent but dangerous and typically wounded animal life. It's not such an unreasonable belief that only a rather specific personality type would be the best in this position, or that having a similar dress code and style of appearance would help reduce stress in said children and animals. Potential Jennys or Joys can wear the hairstyle and assist instead of a conventional Pokemon journey or general schooling, but don't get the full title or uniform, while full Officer Jennys or Nurse Joys have spent so much time in the identity that the thought of removing it to disguise themselves rather than covering the mask is unthinkable.

Pokemon sex and birth is hideous, disgusting stuff that people can't help but block out.
The eggs are between eight and ten inches tall and four to six inches wide. Some Pokemon are smaller than that, and can still have eggs (not including, for example, Oddish's leaves). A full-grown Ponyta can burst forth from one of these eggs, small enough for a ten-year-old to carry five of them outside of a Poke Ball. And don't forget Improbable Species Compatibility. It's got to be traumatizing enough that the Day Care Lady (or guy, in R/S/E) won't tell you anything, even if they can bring themselves to think about what your Tropius did to that poor, poor Oddish... and the bloo- sap- fluids after laying the egg...
 * And don't forget the ability to hatch a a full-size Snorlax from one of these ten-inch eggs!
 * Well, not anymore now that Munchlax exists. Onix, however...
 * It is still possible to hatch Snorlax from eggs (as long as the female in the pair doesn't hold a Lax Incense, you WILL get one). Perhaps Pokemon are born egg-sized, then almost immediately grow to their normal species' size?
 * The Pokemon don't seem to mind. Either they aren't fazed or there is something horrifying about them...

The Pokemon Center and the Rare Candies are part of a plot to rule/destroy the world.
The Pokemon Center saps the mysterious evolution-related energy from the Pokemon a little bit at a time, each time they're healed. The Rare Candies were already around, but Pokemon Centers bought out the brand and the formula so they could add a weakening agent, as well as helping the Pokemarts and Department Stores maintain the cartel that keeps Potions higher-priced than they could be. Now, if you want to raise a Pokemon to level 100 at its strongest, you have to battle. A lot. And get healed. A lot. The battling helps the Pokemon recover from the Pokemon Center drain.

Pokemon are Proud Warrior Race Guys.
This seems to pretty much be their mentality in the anime, and explains why they don't mind being captured and used by worthy trainers (and rebel against ones they don't think are worthy). It also makes the recruitment processes in Ranger and Mystery Dungeon make sense.
 * It would also explain why the wild Pokemon not only attack you when you're walking through the grass, but sometimes make it so you can't run away (like with Mean Look or the ability Arena Trap).

The Pokemon Day Cares are a Team Rocket front.
While it makes sense for some Pokemon to lay eggs in the wild, such as Bird-type Pokemon, there are also Pokemon with certain characteristics that make little sense on what appears to be both warm-blooded and have young 'hatch' at instant physical maturity and able to hunt for themselves. And that's ignoring the rather hefty supply of Pokemon that do have an immature form that they evolve out of due to happiness, gender ratios that wouldn't make sense in the wild, the wildly unusual yet successful alleged Interspecies Romance, or the simple Improbable Species Compatibility. Or the simple part where eggs are so reliably and quickly produced. Or how Pokemon can observe things that occur while still in their eggs. We've even seen records of Pokemon giving birth, albeit only in research documents. And no one has ever seen a Pokemon lay an egg, even though some species are farm livestock.

But we do know of a situation that results in mature Pokemon breaking out of fluid-filled containers at difficult-to-predict intervals, emerging with significant control of their own powers; we've seen it happen before, Gone Horribly Wrong. Only one group has the technology or interest in doing so.

The question becomes why. Obviously Team Rocket gain a lot from maintaining the day care: easy access to samples from some of the strongest and rarest Pokemon on the planet, hand-delivered to them. And cloning Pokemon for their own benefit has obvious results. But what do they gain from releasing a selection of the clones, powerful beings that Team Rocket has had adequate opportunity to brainwash, alter, or implant tracking chips within?
 * The Pokemon actually have two eggs at a time. They give you one, giving you an incentive to give them more Pokemon, and keep the other for themselves.
 * Let me just point something out. Why is it that the woman at the counter has to look left and right? It's as if she's making sure that there aren't any main protagonists here who might expose the day care for what it is!

Pokemon birth is done by magic.
They take a bit of each ones hairs/scales/whatever that gives DNA, a bit of mud, play around, recite some Pokemon magic, and ta-da! New Poke-eggs! That's why humans can't really understand how it happened, because they do it really quick. Male and female designations are given just because they have different gender roles at such playtime (mother's genetic resemblance, father's moveset).
 * This does explain why creating eggs takes varying times among Pokemon species, but not why some Pokemon like each other better than others.

Pokemon have both psychic powers (not to be confused with the Psychic type) and matter-replication abilities.
It explains a lot of the questions under Fridge Logic. It explains why a little turtle can fire a stream of water with fire hose volume, and a horse can move about on water when battling. The field isn't drenched after Surf because the Pokemon that used it turns the water back into energy. The matter created in this fashion can only be commanded by the Pokemon that created it, which is why they can't dispel each other's attacks. The extra mass gained by evolution? Think Animorphs. They pull the energy out of some other space and build their new body according to the protocol in their DNA.
 * It could be that they take everything they need from atmosphere itself. Like water. Yes, you've seen such explanation before.
 * That "other space" bit makes more sense now that Platinum has been released, with the Reverse World. Perhaps as the God of Antimatter, Giratina is the "break the laws of physics to let new matter come into being" god? The smaller size of the Reverse/Torn World would be explained by it only having the equivalent antimatter to the positive matter used in the creation and evolution of Pokemon (if antimatter and matter are being created all the time, but instantly destroy each other, Arceus and Giratina separate the pairs so that they can add the normal matter to the Pokemon universe and the reverse matter to the Reverse/Torn world.)

Humans in the Pokemon world are Made of Iron bordering on Nigh Invulnerable
During Pokemon battles, Pokemon use moves like Sandstorm, Fire Blast, Hail, Blizzard, Surf, Earthquake, and loads of other attacks of that kind. Considering the blanket effects some of these attacks have, it's hard to believe the trainers are totally unaffected. The truth is that humans in the Pokemon world are practically superhuman, capable of feats such as surviving incredibly powerful attacks and breathing underwater indefinitely.
 * This Troper thinks that does explain a few things, like why nobody seems to care about the fact kids are wandering about with a team of living weapons. That also would fit well well with the below WMG, as in perhaps they didn't just bother with weapons because Pokemon are more powerful, but because most weapons would be less effective against someone than, say...Hyper Beam.
 * Come to think of it, this also explains Team Rocket's continued existence and the fact that Pokemon attacking trainers is used for comic relief rather than causing serious injury.
 * Black and White seems to confirm this considering the No OSHA Compliance-ness of the Mistralton City and Icirrus City Gyms. We also see Alder jumping down from a very high cliff to meet the protagonist and his/her rival in which he didn't get even the slightest injury.

The presence of Pokemon stunted weapons development
Seriously, why develop things like swords and clubs when you can command super-powerful beings? That one banned episode of the anime aside, humans in the Pokemon world never developed weaponry like guns. The reason that evil teams let you pass them by once you beat them is because, hey, you have Pokemon ready to battle and theirs are fainted, and no one messes with someone who commands superbeings. No one came up with guns because it never occurred to them that humans could defend themselves from Pokemon with powerful enough technology.
 * Except for some lasers and death rays, of course; because the villains' science is so cliched it would be a staple in every boss' secret room.
 * There was another episode in an early season, with a criminal who is distinctly shown with a gun. It was only a training exercise, as this troper recalls, but the Officer Jenny at the scene distinctly warns Ash about the dangers of attacking an armed opponent.
 * In that case, I assume that firearms exist for those that, for some reason, can't use Pokemon. However most people can, so they're barely used

Pokemon used to fight to the death.
This drove them to the brink of extinction, so humans taught them [how] to defeat their enemies with a Non-Lethal KO instead. This also explains why Pokemon serve human masters - they feel they owe it to the people who saved them from mass suicide.
 * Pokemon DO fight to the death. Read the Pokémon Special manga.
 * Really? And Pokemon training is legal?
 * They only fight to the death as a matter of survival or when villains are involved. They don't do it in normal trainer matches except by accident.
 * This actually makes sense. Almost all Pokemon used to be hyper-aggressive, and would naturally keep fighting as long as the opponent did. Humans intervened eventually, though. They just bred Pokemon that had a lower pain threshhold. They would faint (and be recognized as defeated by the other Pokemon) rather than fight to the death. It was also beneficial to breed those Pokemon that were not so aggressive and violent.

All legendary Pokemon, with the possible exception of Deoxys, are the gods of the Pokemon world.
Canon explicitly states that at least seven of of them (Arceus, Dialga, Palkia, Giratina, Uxie, Mesprit, and Azelf) had a role to play in the creation of the world. However, all legendaries have immense power and control over the world, in the manner of a Physical God. Deoxys is only listed as a possible exception because it's unclear what, exactly, it does or represents. As for the rest of the PokePantheon:
 * Kyogre, Groudon, and Rayquaza seem to be the deities of the sea, land, and sky. It's possible that while Dialga, Palkia, and Giratina created the world itself, it was these three who shaped it into its present form.
 * Heatran is said to have been born from volcanic activity at the time of the creation of the world. Perhaps it's the deity of volcanoes everywhere, or maybe it is simply the god of Stark Mountain specifically. Alternatively, it could be the equivalent of a behemoth from Exalted: divinely created, but with no real purpose behind it and not a god itself.
 * Or it's what Manaphy is to Kyogre.
 * Regigigas is said to have moved the continents long ago, and may be a personification of strength. It created Regirock, Regice, and Registeel in its image.
 * Adding on to that, one Regigigas created the other Regis to assist humans. This Regigigas stayed in the area around Snowpoint with one set of Regis, but the people who lived there eventually became horrified of its power and sealed it away. Knowing that it was powerless without Regirock, Registeel, and Regice, they also hid those three away in areas protected by a seal that could only be broken by Regigigas. What they didn't realize was that the Regis weren't unique, and others lived in faraway regions.
 * Cresselia is the moon goddess, obviously. Her opposition to Darkrai, the deity of nightmares, may indicate that she has some influence over dreams as well. Their residence on Fullmoon and Newmoon Islands, respectively, as well as their respective typing, may also indicate that they are the equal-but-opposite gods of light and darkness.
 * Manaphy may be a sort of aquatic Jesus figure, given its status as a powerful, one-of-a-kind legendary that is born to a rare but otherwise unremarkable species of ordinary Pokemon.
 * Which is still classified as a legendary, mind you.
 * Jirachi is the god and occasional granter of wishes.
 * It may have a connection to the prominence of Stars in other Nintendo franchises.
 * Shaymin is the deity and protector of nature. Celebi is actually the deity of peace and prosperity, as indicated by various Pokedex entries stating that it only appears in peaceful eras. Its association with plant life is mostly symbolic.
 * Shaymin is only around in great turmoil, when the world is in danger. Celebi is only around in a state of peace. They rule dystopian and utopian parts of nature, respectively.
 * Ho-oh is the deity of death and rebirth. Given that Lugia is its opposite number, and formerly roosted in the Brass Tower, which was said in the games to be where Pokemon "awakened", as the Tin Tower was where Pokemon "rested" (phrasing that smacks of euphemisms for birth and death), it's possible that it's the deity of new life, or of life in general. It is, in any case, exceedingly powerful. At any rate, they oversee the legendary birds and beasts, respectively. Articuno, Zapdos, and Moltres represent ice, lightning, and fire; Raikou, Entei, and Suicune represent storms, volcanoes, and the north wind.
 * Latios and Latias are among the only legendaries to have gender, are each exclusively male and female, respectively, and are mostly identical apart from their gender. Accordingly, they may represent the concept of gender, and may, indeed, have been the first beings to be either male or female in any meaningful way.
 * Other sites speculate they may also represent Yin and Yang, which also mean gender.
 * Which is probably all but Jossed with the advent of Generation V's Tao trio.
 * It's worth noting that the Emerald Pokédex entry for Latias explicitly states that they form "herds", meaning they are certainly not unique and therefore making it doubtful that they really fit with this theory (though for the same reasons, their status as true legendaries is debatable.
 * Mew is the progenitor of all non-legendary Pokemon. Mewtwo, despite being man-made, was created from Mew's DNA, and probably counts as divine.
 * Deoxys could be something along the lines of life itself (if you allowed Lugia to be new life). Consider that it's a virus and DNA. Alternatively, it could in fact be a mistake, a creature that the Gods themselves didn't intend to arise.
 * Mewtwo was a very wise Pokemon, but a Pokemon nonetheless, and not truly the Pokessiah.
 * Given his origins and above theories on them, Mewtwo could be the representative of humanity. Possibly a Messianic Archetype, maybe an Anti Christ or Dark Messiah...
 * Or, as Mewtwo is a mon created by science, he possibly resembles "Science" in the Religion vs. Science argument, while all the legendaries are the so-called "Gods" everyone believes in that stand for the Religion argument (obviously). After all, no matter how many people believe Arceus is God, you're always going to have the atheist that will not believe. So Mewtwo is meant to represent that non-belief. Hm...this leads discussion for another WMG coming on.
 * Or what happens when you play God...
 * The pseudo-legendaries are demigods. Garchomp, Salamence, Dragonite, etc., only have mere physical form, but they actually have higher base stats than the Legendary Trio members. I can only conclude that Mew made them first as a sort of police force to keep the Pokemon (and especially the humans) in check until Arceus can come in his human avatar.
 * What about Rotom?
 * Rotom isn't a legendary.
 * Of course it is, it's a wandering Machine Spirit.

The programmers in the game are Physical Gods who laugh at the player's failures
The programmers in the games admit that they created the player and everything around them. They even created Arceus, with the intention of Arceus creating the universe. And because they're magnificent bastards, they created the Eldritch Abomination MissingNo. with the knowledge that they could fix the glitch at any time, but enjoyed watching the chaos he created. And every new generation, they destroy the old universe and make a whole new Arceus to make a whole new universe. In pokeworld, each universe only lasts five years at max. FR/LG is them remaking their favourite universe without the glitches. It's the only one that still exists.
 * Eh, there are too many Continuity Nods for this to be plausible.

The Pokemon world is a social experiment by a post-Singularity civilization in the far future.
This would explain a lot of inconsistencies with real world physics and biology:
 * The world is actually an experiment by curious hyperintelligences wanting to see how a human culture would evolve in a world with real mons. (They engineered the world based on the template of a popular video game/manga/anime franchise from the late 20th/early 21st century A.D.)
 * Most of the inhabitants aren't aware of their world's true status.
 * The Pokemon themselves are genetically engineered creatures with clarketech features enabling their seemingly magical attacks and capabilities.
 * Certain commercial technologies (Poke Balls, etc) are blackbox tech of the same principle(clarketech) and are regulated by the overseers of the experiment behind the scenes.
 * The Nurse Joys and Officer Jennies are all clones created by the hyperintelligences as agents to regulate healthcare/law enforcements as well as a way to gather informations and discreetly control most of the civilisation's crucial infrastructure.
 * The main legendaries (Arceus, Mew, Celebi, Darkrai, etc) are in fact direct avatars of said hyperintelligences. They functioned as psychological focus to exert subtle memetic control (in form of legendary-centric polytheistic worships/animist religions etc) over the local populace.
 * Batches of hundred plus newly engineered species of Pokemon are introduced into the world every one 'generation' as a part of the ongoing experiment.

Gym Badges are also licenses to prove that you have been certified in an out-of-battle move by a gym leader.
Most gym leaders are only trained in teaching roughly one or fewer HM skills. One example, Norman in 3rd Gen could have been trained in teaching Whirlpool, but since there are no whirlpools in Hoenn the demonstration required to earn the Balance badge (summarized by "this badge allows you to use ___ outside of battle") is not included in the expository text. This is why it is possible to get badges without actually winning a match (at least as shown in the anime and the Electric Tale of Pikachu manga), since a trainer only has to prove to the gym leader that they are worthy of 1/8 of the admission to the regional tournament by handling their Pokemon well. This is also how breeders and explorers are allowed to use the HMs out of battle, they just get a non-trainer permit from the gym leader.

Only the wealthy class is able to afford Pokemon training in the games.
In the games, the PC almost always comes from a multi-level house with a large living room, a computer, and a father who seems to constantly be away on work. All the other homes seem to be one room shacks barely able to accommodate a family. Those who aren't rich, but train Pokemon anyway, put their family through serious financial strain.

Pokemon are biologically immortal, and the constant battling with them is population control.
I haven't seen all of Pokemon, not even close. But has there been a Pokemon that didn't die of injuries, disease, or malnutrition? If there is, it could possibly be post-battle trauma or a disease. But anyway consider if Pokemon are immortal this way, eventually they may devour the world dry of resources. From the eggs and Pokemon like Weedle still around, it seems like Pokemon definately breed even though they have the immortality. So the constant battling that has now become a way of life is being used to 'save' the planet!
 * Pokemon Coliseum mentions at one point that Pokemon can live far longer than humans. The old man stating this says that the Treecko standing next to him is ninety years old.
 * But in the anime, Tracey is shown to have an elderly Scyther. If a Pokemon can age, it must be able to die of senesence at some point.
 * They probably age incredibly slowly relative to human lifespans. Heck, Rock and Steel types probably have lifespans in the tens to hundreds of thousands of years.
 * Maybe Pokémon are like the Turritopsis nutricula?

The English language is derived from Pokemon.
People have discussed before that Pokemon always say their names. How do the Pokemon know what their names are? They don't. Most likely, people named the Pokemon after their battle cries.

This brings up the disturbing thought that a number Pokemon cries are terrible puns. Bulbasaur for a dinosaur with a plant bulb on its back? Charmander for a fire breathing salamander? And these things actually say their names? Give me a break. This could not occur in nature. Unless...

The only possibility is that in the Pokemon world, English is derived from Pokemon language and attributes. Other languages would be the same process, but alternate interpretations of Pokemon sounds.

This also explains why more recently discovered Pokemon have less punny names.
 * Oh, they do, just in different languages. So English ain't the only language that Pokemon helped create.


 * Well, there are the Unown, which are literally the English alphabet.
 * There is a flaw in saying Pokemon are named after their cries, as not all pokemon say their name. Krabby's cry is 'Koo-kee', Staryu's is 'H-YA!', and Starmie has it's strange cooing sound.
 * Also, most of the cat-pokemon say "meow/nya;" Lapras "croons;" Onix and other large species just roar; Dawn's Pachirisu and Iris's Axew both make a sound that sounds a bit like "gib-wah."

Say instead, then, that Pokemon species start out with a "cry" that is appropriate for their apparent species...but in associating with humanity, and instinctively trying to communicate better with their trainers, their cry "morphs" into the human name for them, which gets hardwired into the next generation. Krabby is halfway there; originally its cry was just a bunch of clicks, and "kookee" is as close as it can come to "krabbee" now. In 20–30 years, it will finally achieve the "r" and the "b" sounds, and the first vowel will go from "ooo" to "uh" to "ah" to the flat "aa" of Krabby.
 * Some species (Onix, Meowth, Skitty, Staryu, Lapras, et al.) don't possess the genetic disposition to change their cry in that way. Team Rocket's Meowth is an exception, a genetic sport that not only randomly got the gene, but got a "super-effective" version, allowing him to (and giving him an instinctive desire to) learn human language.
 * Alternately: Meowth, the Slowking in Movie 2, and the Gastly in the "Maiden's Peak" episode all awoke their own dormant genetic potential to learn to speak through their fierce desire to do so.

If you fight a wild Pokemon and lose, the Pokemon Center takes half of your money, since they have to revive you AND your team.

 * The games never DO say where the money goes... it would explain how they keep the centers up and running.
 * Maybe this is why Nurse Joy always says, "Hope I'll see you agian". It's already implied sadistic intent, however this is more or less directed to the hope that you will be defeated and injured by a wild Pokemon so that they can steal the money off your unconscious person, rather hoping that just your Pokemon alone get hurt.
 * Jossed. The 4th gen games say that the trainer drops the money in a panic (I learned that when that little bastard Azelf kicked my ass. MULTIPLE TIMES >.<)
 * I never got that. How do you drop money in a panic unless you have it out in your hands? Wouldn't you be, I dunno, keeping it in a wallet in your bag?
 * Well, you're obviously carrying two wallets; one in your pocket or backpack and one you carry around in your hands for immediate expenses. You make sure to split the money evenly between the two, so that if you should lose one wallet you still have the other. ...It makes sense, I tell you! It makes sense!

Pikachu is the only Pokémon that says it's name only

 * If a cat can speak English or Japanese that it would be too hard to teach a rodent to say Pikachu.
 * In Pokémon yellow Pikachu's the only one who does that the others just grunt like real animals.
 * Ash's electrocutions to make him think all other Pokémon do the same.

Legendaries DO breed, but...
Legendaries have genders and do breed, like the Lugia with the baby, but any number of the following things happen.
 * 1) Legendaries don't deem non-legendaries worthy of breeding with them. Also, this is why Attract doesn't work on them.
 * 2) Non-legendaries find legendaries too scary/ugly/intimidating to mate with.
 * 3) Day Care employees don't allow legendaries to breed, to control legendary population.
 * 4) Day Care employees don't trust legendary eggs to ten year olds.
 * 5) Team Rocket/Aqua/Magma/Cypher/Galactic buy/steal/are given legendary eggs from the Day Cares.
 * 6) Legendaries never let ANY humans find their eggs.
 * Manaphy is, of course, the exception.
 * Maybe their mating process is so different from other Pokemon mating processes that it can't occur in the same scenarios, for example; Palkia, Dialga, and Giratina are three genders of the same species, after they mate Giratina goes off and forms an alternate reality cocoon and pupates until a baby Arceus is formed. Arceus is known to be able to produce those three as well. A number of real world species have a sexually reproducing/asexually reproducing life cycle (though none in the animal kingdom as far as I'm aware). The Regi's probably have a vaguely similar, albeit slower, system, with Regigigas in the process of creating a Regice. Shaymin only turns into its sky form when it's exposed to a Gracidea flower, let's say those are actually the flower from other Shaymin, this fertilizes them and then they become able to fly in order to spread the resultant seeds.
 * Oh, and those particular mating theories may not work for the anime or manga. I consider them each to be separate canons and am personally only interested in game canon. Just so you know.

Even among humans, daughters always look like mothers
See: Jennys and Joys.

"Shiny" is the Pokemon equivalent of Albinism
Think about it, the rarity of catching one, and even if the color difference is minor, they still produce sparkles. The reason they are rare in the wild is the fact that a shiny Pokemon would be picked off by predators if it's prey, and there has to be some issue its health if the Pokemon is based off of a predator.

You never caught any of the Legendaries.
Seriously, the game actually thinks that a 10-year old boy with less than a year of experience can capture a rare powerful beast? I think not. All those ones you caught were fakes. The same goes for Arceus. Think about it this way: Can a mortal man control God? Absolutely not.
 * How would you know? How many people have tried that in reality?
 * There was this one guy...

Legendaries aren't "caught", they consent to follow the player character.
Going off the above theory, it does make little sense that a legendary Pokemon, especially ones like Giratina or Arceus, could be controlled by human technology like normal Pokemon. Instead, they probably allow themselves to be "caught" after recognizing the player as a Worthy Opponent. They probably make a unspoken contract with their trainer, that they agree to fight for them for the extent of the lifetime of that human, but if they dislike their trainer, that human will experience, at best, a painful death.

Formalized, competitive battling is a recent development.
I should mention that this especially applies to the game world, but may not hold up in other adaptations. I've only played the games.

People have, of course, been taming and even battling with Pokemon for ages, but it's only with recent developments in PCs and Poke Balls that League-style formal battling has become feasible as a sport. Silph Co. appears to more or less have a monopoly on the Poke Ball market, which suggests a new technolgy, and in each region the programmer of the local PC network, implied to be the original developer, is not only present but quite young. Pokemon Centers, with their ubiquitous PCs and dependence on Poke Ball technology (they never take the Pokemon out of the balls), may be a recent development as well.

Where before, people were limited by what Pokemon they could easily travel with - very large Pokemon or Pokemon that are composed of or give off hazardous materials, such as many fire- and poison-types, would be difficult to take places if traveling on foot - the new, stronger Poke Balls and the PC network make it possible to have any Pokemon with you anywhere. This allows the building of bigger teams and makes it feasible for the average trainer to travel much farther and over rougher terrain to find opponents - imagine traveling a water rout with a high-level team all outside of their Poke Balls!

This also explains why many trainers have only two or three Pokemon, and why so many NPCs fail to take you seriously - you're young and have easily adapted to the idea of effortlessly carrying up to six death-beasts with you anywhere, and probably more if it were allowed, but most of the adults are still stuck in the mindset that two or three Pokemon are enough for anyone to keep track of and that if you can't see someone's Pokemon with them, they probably aren't that impressive.

The Pokemon World is Our Own Post-Apocalypse, Thanks to Arceus
Modern day Earth is going to hell in a handbasket thanks to humans, take your pick at the cause. Regardless, the world is in 'chaos'. One day, an egg suddenly appears from the sky in what is now the Shinto Temple in Japan. Arceus hatches from the egg and unleashes its judgement upon the world (think Day of Lavos), destroying human civilization overnight and bringing 'order' to 'chaos' in Arceus's view. Using the Shinto Temple, it then creates its servants. Palkia, Dialga, and the lake trio are born under Arceus's control. Giratina, though also born at this time, is not. Arceus commands the dragon trio to destroy the remains of human civilization and bring any survivors to it. Palkia and Dialga do so, but Giratina sees the destruction Arceus has caused and rebels. Arceus banishes it for this. The remaining humans are then rounded up and any trace of their former selves or knowledge are erased by the lake trio. Its task complete, Arceus and the two dragons disappear from the world. What animal life existed at the time start to become Pokemon after being exposed to Mew's species, who was either hiding on the planet all along or arrives from space to inhabit the planet shortly after the destruction. Lacking any knowledge of their prior technology, humans begin to rely on these new creatures to survive.

A really big freaking theory on a lot of things
Okay, just to forewarn any and all readers: this will be long. As the name suggests, this is an attempt to bring multiple threads together to weave the rather bare-bones mythos into a (mostly) coherent whole.

So, let's start with the origins of the Pokémon world. Suppose that a long time ago, there was an Earth-That-Was situation. Humanity evacuated to find a new world. This world, naturally, would be the Pokémon world. The planet was terraformed with certainâ€¦ devices (we'll return to this later) and reshaped into a roughly Earth-like format. This is why certain regions correspond to actual locations in Japan, and why Orre is like Arizona. Also, certain regions were named for their Earth-Prime (as we'll call it for simplicity) counterparts. Ever wonder why there are references to China, South America, and various other Earth locales in the Pokedex? This is why- some of them are in fact referencing the Earth-Beta locations. Lt. Surge is from America-Beta, and fought in a war on the game's planet at some point in the past, but it's just called America due to years of just calling it America and what have you. Of course, not all regions have their Earth-Prime names, whether because of people becoming original with the names or the pronunciations becoming corrupted- like Orre for Arizona or Phenac City for Phoenix. By now, though, a lot of this has been forgotten, due to thousands of years passing.

Ah, you say. But you mentioned terraforming. What's up with that? Glad you asked. Simple answer- Regigigas was part of the machine. Consider, for a moment, that Regigigas takes a while to start up, rather like a not-so-good computer. Also consider that it requires three keys of sorts to start up, the golem trio. Finally, Regigigas has plugs for hands. It's mentioned in the dex that Regigigas moved the continents by towing them with a rope- however, again due to the telephone-game effect, it was actually a device called the R.O.P.E. that Regigigas used to tow the continents, by plugging its hands into it. While seemingly organic, Regigigas and its trio are all bio-organic machines, perhaps created from materials found on humanity's new planet. It's unknown what Registeel eats, and Regirock can repair itself with boulders, so there seems to be both machine and living being there- and their Clear Body abilities are shared with the Beldum line, the only other robotic Pokemon. Consider for a moment that they were originally simple automatons, but of course A.I. Is a Crapshoot and they gained sentience, possibly turning on their masters. The Braille in Hoenn suggests the Regis were sealed out of fear of their power. And what better way to make sure the strongest one is kept locked away than by hiding its three keys in separate regions? The legends were passed down to keep people from unleashing this power again, but so much time passed that all the warnings were naturally forgotten.

Now, the technology rant leads us to our next segment- why are the levels of technology so random? On the one hand, humans on the Pokemon world can capture giant animals in baseball-sized capsules and have teleport pads, but there are few motorized vehicles seen and TV and radio are at the same level as the real world. My conclusion is that some sort of disaster- in fact, perhaps the possible golem rebellion- ended up destroying part of the technology humanity had developed, and so in some areas we were set back while other advances were mostly intact. Of course, it wasn't perfect, since Poke Balls had to be made of apricorns for some time until technology advanced back to a suitable level, but it worked. Less vital things, like aforementioned forms of entertainment, were either mostly lost or considered unnecessary luxuries and mostly ignored while humanity recovered and did more important things on their new home. Of course, if the above is true and the Regis are all manmade, then this means that Porygon isn't the first artificial Pokemon.

Now we come to the Pokemon themselves. While sometimes we seem to think of them as aliens, like the Clefairy, humans are in fact the aliens to Earth-Beta, with Pokemon the native inhabitants. Unfortunately, while Pokemon used to be treated as equals, as legends in the Canalave library describe, years of slow, somewhat unintentional subjugation has led them to take on more or less pet roles. In a time when people used to let Pokemon sit at the same table as them, now they are given nicknames and have had their growth as a species stunted to the point where they can only say their own name. Of course, this isn't a violent or cruel thing, for the most part, but the species as a whole has lost out on a great deal of possible progress. Humans may have been more inhumane to Pokemon at one point, as the legend of the man with the sword implies, but this is no longer the case. However, some Pokemon are not native- Deoxys, for example, is a space virus that mutated. However, if there are multiple life-supporting planets out there, why do all the apparent deities reside in one? Two options- either the Pokemon world was in fact a sort of Mount Olympus/Valhalla combo for the gods and their creations in their own image to reside in, or Arceus and co. are only the gods for that particular planet. Consider the possibility that there could be more than one Arceus-like being- the gods of various legends on Earth-Prime are the counterpart of Arceus, and Groudon/Kyogre/Rayquaza are literally the Behemoth, Leviathan, and Ziz of Earth-Beta. And so on and so forth, naturally. As for Clefairy being on the moon, perhaps they had the capacity for short-range space travel at some time in the past, and the humans had a moonbase while terraforming. The Clefairy could have helped out the humans, and over time the stories got muddled into Clefairy being from the moon, while humans were native.

A few other short theories/ideas that fit into this:
 * Terraforming done by Regigigas caused a misunderstanding between Groudon and Kyogre, which led to their battle. This may also be why the trio is hidden in Hoenn while the trio master is in another region- so Regigigas wouldn't go tick them off again.
 * Arceus was initially opposed to humanity- it's been suggested that Giratina is the Pokemon who appeared to the sword-wielding human to show him the error of his ways. Giratina honestly doesn't seem that bad in Platinum, after all. If Arceus didn't like humans, then perhaps this is why Giratina was banished and is known as the Renegade Pokemon- for showing kindness, rather than violence as the famously-inaccurate Pokedex says. Dark Is Not Evil is a trope that Pokemon has demonstrated before- perhaps people just saw images of Giratina and jumped to conclusions.
 * Way back in Kanto, there's a guy who suggests he saw the space shuttle take flight back in the sixties. Either there was another shuttle launch in the time deemed the 60s on Earth-Beta- unlikely, as the flights seem to be unmanned, ignoring the anime having astronauts; of course, the guy could be crazy, or he's just joking around with a naïve ten-year-old. It's probably the latter. also, the model of the Columbia is kept as a memorial of one of the few Earth-That-Was things that is still well-recorded.
 * What, you're looking for some humor in this? Fine, if you really want it. Looker is the Doctor and the Trick Master is the Meddling Monk. Happy?

That's about all, finally. Feel free to pick apart as you will.

The legendaries were created by belief
The Legendary Pokemon did not exist until mankind (and possibly Pokemon-kind) believed in them. The legendaries are, in fact, powered by belief. They can use all the powers mankind would expect them to have, but because they require man's belief, their actual abilities are finite. Dialga, for example, can control time because that's what mankind expects, but it never actually created time. Arceus can use abilities like Judgement and create the other legendaries because people believe it can. Groudon never created land, but it can create land. The conflicting backstories for the various legendaries are because the legends themselves conflict: the pokedex is just spitting the legends about the Pokemon back out at you.

The various incense items (Sea Incense, Lax Incense, etc.) are psychotropic drugs to Pokemon.
Certain Pokemon seem to have real affinities for them, but look at Happiny, Azurill, and Wynaut as proof. Unless one of the parent Pokemon is holding/using the incense, their "evolved" forms hatch from the eggs instead. And these species require special care before they can develop normally. So what does that mean - the trainer artificially induces what could be considered birth defects when he/she breeds them.

The reason Pokemon learn moves when they do is because of the Pokemon Trainer's skill.
Or, in the case of wild Pokemon, their skill. It explains why Lance makes his Pokemon learn moves at the wrong levels and why some Pokemon know things they shouldn't. It's like adaptation, but... well... better.

Team Rocket is actually a well equipped mercenary force disguised as black marketeers
. Several times in the anime, they have been shown using mechs, subs and jetpacks. Obviously, none of those items are cheap. Black marketeers would have no need for such expensive items but mercenaries would. It would also explain why the police cannot seem to take them down. I mean, what police force could stand up to an entire army?

The Pokemon and humans are actually made of self replicating nanomachines.
This explains why Pokemon can be healed instantly by Pokemon Centers, why there is no "real" wildlife, the way Pokemon of all species can communicate, how Skitty and Wailord can breed, and why they can unleash huge amounts of energy without a source. Pikachu doesn't cause heart attacks, they breathe in volcanoes, and all have psychic powers. Because they are nanomachines they can "eat" each other, become "ghosts", "reproduce", and fit into Poke Balls. Why can Pokemon do weird things like enter dreams, hypnotize, teleport, learn from CDs, become ghosts, evolve, shapeshift, and fly? They are nanomachines. They can simply rearange themselves when necessary. The only real things seem to be water, some random foliage, mountains, and air. Perhaps the purpose of their existence is to terraform the planet for the true humans. Arceus is likely a supercomputer in control of everything. Once the true humans arrive, they may or may not turn everything off, thus ending the inhabitants existance forever.
 * On the bright side though, they might get reused elsewhere.
 * Perhaps each generation is a new planet? The human overlords can duplicate a terraformed region, but need the nanobot species to beta test the next expansion. Maybe there are only even two planets, and the humans and nanobot species switch back and forth?

Extingishing a Charmander's tail is not fatal; this lie helps protect both Charmander and their trainers.
As seen in the Pokémon Mystery Dungeon games, Charmander can have their tails get wet—even completely submerged—without immediately dying. Trainers are simply told otherwise in order to teach them caution. Remember, the starting age for trainers is canonically ten, and you run into some trainers that are much, much younger. Mons are dangerous enough without giving a fire-breathing lizard to some curious kid who might want to play with his new friend's pretty tail...

So they say "Hey, kids! See your Charmander's fiery tail? If it goes out, IT'LL DIE. So be careful, won't you? :D" And the kids are a little psychologically scarred, but hey, that's better than burning your hands off, right? To say nothing of how an irritated charmander would likely react to some brat toying with or even yanking its tail... Even if the charmander doesn't retaliate, once it evolves... See what happened to Ash. But this way, the kids know to be cautious, and will hypothetically treat their new charmander with extra care.

In fact...

All of the entries implying that somebody harmed a Pokemon are actually meant to dissuade that behavior.
Because children aren't alway innocent—they can be cruel, sometimes horribly so—and even when they mean well, there can be problems. To combat this, several PokeDex entries casually mention some of the consequences of this sort of experimentation... like, say, what would happen if you cut a Raticate's whiskers off.

...Admittedly, this doesn't do much for the brats who want to see if that'll really happen, but at least this way they can't say they weren't warned.

Pokémon ate from the Tree of Life instead of the Tree of Knowledge
Alakazam is supposed to be a mega-genius with 5000 IQ, other Psychic-types are probably similar in intellect yet we never see them build cities like those of humans (ignoring the spinoffs here, speaking strictly about the main game continuity). Why? Because for however "intelligent" they are, that intelligence is directed towards their psychic powers rather than understanding. When the Pokémon world's equivalents of Adam and Eve ate from the Tree of Knowledge and sought to understand, their primitive Pokémon companions ate from the Tree of Life and sought to become more powerful. The Pokémon grew to gain powers like evolution and the various moves, while humans grew to build more and more complex tools. In a possible example of Linear Warriors, Quadratic Wizards, humans eventually built items like the Apricorn Ball and later the Pokéball to gain control over the world's Pokémon. A world dominated by power came under the control of those with understanding instead.


 * How do you explain Uxie, then?

Aura powers Fighting, Dark, and Psychic types, but in different ways
This explains why they typically have Personality Powers and why they have type match-ups like they do, because of hiow one part of the soul affects the other.

-In the anime and games, it's clearly shown that aura based moves take shape in Fighting type moves, as evidenced by Lucario's Aura Sphere. However, it actually provides the powers of all fighting types, simply in different ways. their training which apparently results in Charles Atlas Superpowers is actually tightening their connection with aura, giving them powers. Lucario's simply manifest more directly. This explains the MASSIVE physique of most Fighting-types.

-Likewise, Dark-types draw on another part of their body for power, their instincts, or spirit, while Fighting-types use their physical body. Their instincts take form in Dark-type energy, explaining why the less powerful Dark-types simply have enhanced abilities relating to thievery and dirty tactics, while powerful Dark-types actually have shadow powers. The type reflects that, as bad Dark-types are shown to be survivalists and thieves, while noble Dark-types like Absol have powers relating to instinct.

-Psychic-types thus use their minds to connect with aura, giving them their abilities. With weaker psychics, this power is a not quite visible form of ESP, but with powerful psychics such as Mewtwo, they can form physical structures with their minds, like Psystrike and Psyshock. The reason some are weaker than others all has to do with intellect, hence why the intelligent Mewtwo and Lugia are the most powerful Psychic-type Pokémon.

-Ghost-types use their emotions to connect with their aura, providing them easier connections to aura, as there is no training required. This explains why most Ghost-types that explicitly aren't spirits returned from the grave, like Gengar, are very emotional and mischievous, while returned spirits like Spiritomb and Dusknoir are more serious about their goals.

Humans have an ability like Pokemon.
Their ability is Shadow Tag. That's why you can never run from a battle. In humans, this ability only deactivates when both are willing. The reason why your presence doesn't trap Pokemon is because human abilities can't affect other Pokemon.
 * Their other ability, much rarer or perhaps the Dream World Ability, is Dimensional Scream.

Pokerus is a Pokemon.
Specifically, the baby form of Deoxys. It's too small to see, let alone catch, and since Deoxys is a Legendary, you can't breed for it. The method that makes it evolve hasn't been seen in any of the regions thus far.
 * "Pokerus, the Symbiotic Pokemon. It can't move on its own, so it attaches itself to passing Pokemon, enhancing them in exchange."

Pokemon Type is rooted in DNA.
Specifically, in a set of seven base pairs, or rather, two sets of three and a "Normal expresser". In each set of three base pairs, each of the sixteen possible letter combinations of the first two results in one of the sixteen elemental types. The third base is a "knockout". If it expresses as "on", the type expression for that set of three is Normal, otherwise, it expresses the type determined by the preceding two bases. So if, say, A and T represent "on" for the type knockout base, then if AA codes for Fire, AAG or AAC would yield the Fire type, while AAA or AAT code for Normal. The second set of three determines secondary type, though if it codes for the same type as the first set, the Pokemon is mono-typed. The seventh base (the "Normal expresser") is another "on or off" gene, which determines if a Normal-type 3-base set will be expressed as part of the Pokemon's actual type, as it is in Normal / X Pokemon like Pidgey (Normal / Flying), Bibarel (Normal / Water), Girafarig (Normal / Psychic) and Deerling (Normal / Grass). It could be that the reason we've never seen a pure Flying type, is that the Flying gene is "delicate" and needs another type, or the Normal expresser active, in order to be viable.
 * What? No. DNA is merely the template for making proteins - it's the proteins that do all of a living system's dirty work, so to speak. You Fail Biology Forever!!!!!!!!!!!!!!!!!
 * Original poster here. When I say, "codes for a type", I mean, "codes for the construction of organ systems associated with a given type and its moves". It's Art Major Biology in any case, so please conserve our precious supply of exclamation points.

The Missingno "glitch" was actually an unintended Final Boss Preview for the final game in the series, and Glitch City is the Very Definitely Final Dungeon.
Okay, let's look at this for a second. Missingno is a Cosmic Horror capable of warping reality, as seen with the item duplication and the Pokémon above Level 100. Glitch City is the kind of messed up place that Missingno would live in.

Now, while the idea of a Lovecraftian-esque Pokémon wreaking havoc on an innocent world may seem a bit too much, remember that this is the series that gave us Cyrus and Cipher. While, yes, Pokémon is primarily marketed as a kids' series (with hidden depths for the "Stop Having Fun!" Guys), the Sinnoh games and Colosseum and XD have been pushing the series into a Darker and Edgier direction, which what is essentially Pokethulhu would end quite nicely.

Wherever the game takes place, be it an existing region feeling the effects of Missingno's existence or somewhere new, the goal of the game is not purely not to become the Pokémon League Champion (though Pokémon gyms are still commonplace), to catch them all or what-have-you. The goal is a much more standard save-the-world routine, with the Cult of Missingno being the primary antagonists. The protagonist travels around the region searching for the entrance to Glitch City. However, Glitch City is blocked by the Pokémon League, with the regional Elite Four and Champion acting as guards (to keep the monstrous Pokémon of Glitch City in Glitch City, and to keep inexperienced trainers out of harms way). Defeating them is a sign of the protagonist's strength, and they are then permitted to enter Glitch City. There, they must make their way to Missingno while fending off the last and most dangerous members of the Cult and the wild Pokémon strengthened by Missingno. Then Missingno is finally seen, first in a human form before transforming into the bizarre... thing we've come to know, love and abuse so horribly over the years.

And it cheats, as is only fitting. Instead of merely having four moves, it has every move known to... whatever it is, which is likely all of them, It's stats are far higher than anything else in the game, and it can't be caught. Whether stated or implied, Missingno is somehow killed by the protagonist's team, and Glitch City begins to collapse without Missingno's power supporting it. However, because this is Pokémon, and the hero always triumphs, the protagonist escapes before it completely collapses, he is haled as a hero for all time, yadda yadda yadda. Then whatever postgame there is is unlocked. (Though that leaves the question of "if these guys are so strong, why didn't they fight Missingno instead?")

... Okay, it's highly unlikely that this will ever happen (A final Pokémon game? Yeah, right.), but the troper behind the idea was rather tired at the time and figured he'd share his sleep-deprived brainchild.
 * Actually it's more likely than it seems. Why? Because...

The games will end at 999 Pokemon.
There just isn't enough coding for a 1000th Pokemon.


 * You're off by 32,001 Pokemon. Note that every Generation has a different number of Pokemon that has never been (and will never be) below 100 and that the total number has so far never ended in zero.

No 'Legendary' Pokemon is actually unique/one-of-a-kind; they just live beyond the boundaries of human civilization.
Breeding Legendaries is impossible because humans don't know any of the requirements or have the proper resources. And given how powerful these Olympus Mons are, it's not like anyone can force them to breed if they don't wish to.

On top of this, none of the Legendaries are actually GODS; those are just titles humans assign them because of their vast power and rarity. Most people would likely go their entire lives without so much as a glimpse of one of these creatures (save for, of course, when a particularly devoted trainer manages to catch one and goes around roasting random Zubat for kicks.

For that matter, the Legendaries that DO get caught? Reckless kids who ignored their parents' warnings about those "tiny but dangerous creatures" and went there anyway. "Ha ha ha, I'm busting all your baaaaallllllls... OH SH--"
 * Alternately, the Legendarys come from the moon, and only one of each is allowed to live on Earth.

The legends ARE true, but the trainer never actually encounters the legendaries mentioned in the Pokedex.
Basically, what the trainer encounters are weaker versions. I shall give a breakdown:
 * Articuno, Zapdos, Moltres, Mewtwo, Entei, Raikou, Suicune, Ho-Oh, Lugia, Latias, Latios, Kyogre, Groudon, Rayquaza, Jirachi, Uxie, Mesprit, Azelf, Cresselia, Darkrai, Manaphy, Heatran, Regigigas, Shaymin: They bred, and due to inbreeding (to keep their line pure)/breeding with Ditto (Ditto may not be able to copy their true powers and strength), it led to weaker Pokemon, with these ones occasionally breeding sterile Pokemon (the ones that the trainer catches, sans Manaphy). For the Weather Trio, this happened before the huge fight. With the Lake Trio, they suppressed their powers before breeding with Ditto. Manaphy is the perfect support, since breeding Manaphy produces the weaker Phione. So presumably, the true Legendaries could look different. This explains why Pokemon like Groudon are said to have created land, yet can only manage to bring up a bit of magma and make the sun shine brightly, or why you can use Tackle on Mesprit or Azelf without zany repercussions.
 * Celebi, Dialga, Palkia, Giratina, Arceus: Time travel/dimensional warping led to them accidentally creating weaker clones of themselves as they disrupted the space-time continuum, hence why you can capture them, and why, instead of warping things immediately, all Dialga and Palkia manage to do is make the sky turn pretty. The Celebi clones are obviously able to go through time as well, but not over long periods of time like the true one can. Of course, this leads to the scary implication of a Giratina that can do even more damage...
 * Mew: Never been implied that there was only one/that it had supernatural powers.
 * Regirock/ice/steel: The Pokedex implies that Regigigas created them. So ancient humans could have used them as templates and made many of them (obviously weaker since they weren't as skilled as Regigigas) as keys for the weaker Regigigas and as decoys to hide the real Regis so some idiot trainer doesn't let out a massive powerhouse capable of moving whole regions by itself.
 * Deoxys: Gets its own WMG...
 * Mewtwo: This one is pretty obvious. Not only is this Pokemon a clone of a legendary, but he creates clones of other Pokemon in the very first movie! Like it's not possible for him to create weaker clones of himself to give to each new 10 year old kid that has been fighting against Team Rocket. He's most likely only giving clones away just to make sure that Team Rocket will not come back, and what better way to screw the Rockets over by letting a 10 year old pwn them at every attempt? In fact... he could very well be working in with the other TRUE legendaries and making weak clones of them, too, just to throw everyone off.

Pokemon evolution revolves more around shutting down genes than adding new genes to the genome.
First of all, it is said that Mew, the so-called "first Pokemon", has the genes of all other Pokemon within it. Second, the move Metronome is said to work by activating dormant parts of the brain, implying that every Pokemon knows every move, but just shuts out most of them for some reason. Other Pokemon could have evolved from Mew by shutting down parts of Mew's genome during development, causing a change in form and what types of moves become available. This sort of thing happens in real biology too, so it's not that Farfetch'd. Of course, because all Pokemon are one species, new species of Pokemon would be better termed "breeds" or "subspecies", and variants within an evolutionary chain would be better termed "morphs".