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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
Pokémon Red and Blue
This page deals with Wild Mass Guesses for games and species in the Kanto/Indigo region. For non-game and non-Kanto game WMGs, please refer to the appropriate page in the Pokemon WMG Index.

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    Generation I Species Guesses 
Blastoise was originally intended to be pronounced Blastiss
It goes along with the theme naming scheme; Squirtle and Wartortle are obviously puns on "turtle", and Blastoise seems to be a pun on "tortoise", which is pronounced "Tortiss". There's no doubt that the official pronunciation is Blastoise, sounding like it's written, but I'm thinking the guy who came up with the English version's name originally had the pronunciation "Blastiss" in mind, but it was mispronounced so often the official pronunciation eventually stuck.
  • It can also be pronounced the same way as Blastoise is (Tor-toise), so I highly doubt it.
Cubone's skull isn't from its dead mother, it grows as a protective shield.
It grows from the back of its skull or something...

Cubone's skull is an external skull which protects its brain.
  • A skull that is internal would also protect the brain.

Slowpoke are Omniscient.
Slowpoke is called the Dopey Pokemon, and every Pokedex entry mentions it being absent minded and airy. Imagine this though: they are so slow to react to the world because their brains are sensing everything that is happening in the universe that their mortal minds cannot possibly begin to be able to process this constant bombardment of information, explaining their lack of attachment to the world around them. When a Slowpoke is bitten on the head by a Shellder and becomes a Slowking, Shellder's venom actually impairs Slowpoke's brain and brings it to a level it can function, turning it into one of the most intelligent Pokemon in the world.
  • To go further, when a trainer issues a command, the Slowpoke can't use the move by memory, its brain is too overloaded with the horrors of the world to remember anything. However, it sees a vision of another Pokemon doing the same move it was told to do, and instinctively does the same thing. Meaning it could potentially perform any move at any time.
    • This works in the anime, but in the games it has a hole: limited PP for moves.
      • I always thought PP was just that the Pokemon would become exhausted from doing the same move over and over
  • So Slowpoke were created by Uxie?
  • ... Shellder have venom?
    • Yes, it's stated to be why Slowking are so intelligent.

The Slowbro you evolve possesses a fake Shellder.
This may go to explain why you evolve Slowpoke by leveling it up, even if you're nowhere near a Shellder. Slowpoke wouldn't know that it's a fake Shellder, and evolves.

Parasect is not possessed by the mushroom.
In the anime, its evolution was treated as a good thing. And in the games, it still has the same personality, friendship values, and everything. While the fungus has taken over the insect's body, the insect's brain has taken full control of the fungus. So it's not a takeover, it's a merger. The insect and the mushroom are synonymous with each other now. But it does have to change its habits to accommodate its new form, which along with its blank white eyes may have led the Pokedex writer to assume it was zombified.
  • Or maybe Paras has always been controlled by the fungus. The fungus it's based on takes control of its victim's mind long before the fungus itself is visible, and with Paras/Parasect the fungus is always visible.

Cubone's skull shape is not literally from its mother.
Instead, each Cubone has a slightly different skull shape. When a female breeds with a male, whichever shape the female had is passed down to its offspring, instead of losing its own skull. As for the male Cubone/Ditto problem, it inherits its father's skull, but only because the Ditto perfectly copies the father's DNA, save for the chromosomes that change it from male to female.

Cubone's headgear isn't actually its mothers skull...
Instead all Cubone heads are exactly the same shape as their mothers'. They're also soft and squishy, so the mother makes a stone helmet, using her head as a template.

Some Cubone get their skulls from their mothers.
And some don't. There are several ways that Cubone could get their headgear:
  • From their fathers (if they have a Marowak dad)
  • I believe the Soul Silver dex entry mentions a Marowak graveyard. Some Cubones may go there to get a skull helmet.
  • Given how Cubone clearly has to have its own skull inside its head... Its possible that, when it has one child, it gives the helmet it used to wear to it. Then, if it has a second child, that's when it dies and gives away its own skull.

Blastoise's cannons are made of bone.
It hasn't been given a Steel sub-type in Gen. II, so this guess would make perfect sense.
  • Blastoise's water jets are said to be capable of cutting through steel and concrete: bone is simply not a durable enough material to withstand such forces. Blastoise's cannons COULD however be made of keratin, the substance which comprises reptile scales (as well as nails/claws, beaks, and hair), which is ounce-for-ounce tougher than steel.
  • A keratin structure with the same design as bones would make sense considering that because of their arched structure, bones are stronger than anything that we could create today with the same exact substance.

Unattended Poké Balls serve as the beginning of the Voltorb-Electrode evolution tree.
If sandals and umbrellas can become tsukumogami, why not Poke Balls? The ones in the past with Young Prof. Oak weren't new and used electricity. Given that the humans of the world have access to electricity via crazy little yellow rats et al, it's not unreasonable that they had access to useful technological applications before the norm.
  • More evidence for this can be found in the various Pokédex entries, specifically Silver ("It was discovered when Poké Balls were introduced. It is said that there is some connection"), Crystal ("During the study of this Pokémon, it was discovered that its components are not found in nature"), and Ruby ("Voltorb was first sighted at a company that manufactures Poké Balls. The link between that sighting and the fact that this Pokémon looks very similar to a Poké Ball remains a mystery").
  • Or...

Voltorb and Electrode are synthetic Pokemon.
Silph Co. engineered a Pokemon that would eat scrap metal and plastic until it builds a shell of sufficient density, at which point it lacks the flexibility to move and eventually dies of starvation. The shell is pried open, hollowed out, fitted with electronic components, and voila- a cheap and effective replacement for the nut-based Poke Ball! Voltorbs are the result of an early design that was hardier than expected, and managed to continue growing and keep its shell flexible by periodically cracking it with powerful explosions. Hence, Voltorb and Electrode's tendency to self-destruct constantly.
  • The shell crack is also how some other Pokemon detonate - Geodudes, Pineco, etc. blow off their outer layers of stone (or bark, or whatever) with shaped charges when they use Selfdestruct or Explosion.
  • Or...

Voltorb and Electrode are the thrown Poke Balls you don't get back
After attempting to capture a wild Pokemon it absorbs the data from said Pokemon and mutates into Voltorb or Electrode based on the data collected. Said Mutation would take some time to happen, or it might be instant, thus the reason you don't just got pick up the lost ball after the battle. Either way it would explain two things, why lose your balls, and why there are so many Voltorbs in buildings...
  • Or...

Voltorb and Electrode are Poke Balls possessed by Ghastly/Haunter/Gengar
And that have become stuck because Poke Balls are designed to capture Pokemon, but because they possessed them they became "captured" in the Poke Ball, and cannot escape it. It's especially noticeable if you look at it this way: Look at Haunter, specifically it's eyes. Put them onto a Poke Ball. You now have a Voltorb. Electrode's habits of blowing themselves up for shits and giggles also seems to fit in with the Ghastly line and their habit of pranking everything. That or they explode because they're really fucking annoyed at their current situation.

Zubat are the Metroids of the Pokémon world.
Not in purpose, but in their method of survival. Consider that they appear in just about every cave environment in the game. The vast majority of these caves contain no noticeable plant life or primary consumers thereof; several of these caves contain few to no "soft" creatures, instead having mostly Rock- or Steel-type creatures like Geodude, Aron, etc. Knowing this, it's safe to assume that Zubat subsist on Hit Points and are otherwise at the bottom of the food chain in their natural environments.
  • Maybe they're like Metroids in original purpose, too. If too many Zubat get caught, bad things happen.
  • If they're anything like real bats, they rest in the cave and fly outside to find food.
    • The problem with them leaving the cave to find food is that some of the environments outside the caves would not contain sufficient small Pokémon (there never seem to be any non-Pokémon animals in the games) or have ridiculously harsh conditions (such as the freakin' blizzard outside the upper floors of Mt. Coronet).
      • Zubat (and its evolutions) seem to be the Pokemon world's vampire bats, so its prey wouldn't need to be small. As our vampire bats feed on cows, perhaps the Zubat feed on Tauros or Miltank, and have similarly pain-numbing, blood-letting saliva.
  • Well... Diglett look soft.

You can't put out a Charmander's tail fire with water.
We all know that "A Charmander dies if its fire goes out". However, this could be interpreted in reverse to mean "If the tail fire goes out, it means they're dead." So the fire could simply be a measure of vitality, and not the direct cause of it. Either that, or it's a lot harder to put out than by splashing water on it or even submerging it. A popular theory as to why Charmander go to great lengths to stay dry is that getting dowsed with water, especially on the tail, really friggin hurts.
  • Or they're scared, which is reasonable for a Fire-type. Look up Hydrophobia sometime.
    • So, if we put ten or so Charmanders on a magic lens and made them stare down into the ocean, their fear would turn it into a hovercraft?

Chansey and Kangaskhan breed through parenthogenesis
This is how they produce offspring without any males
  • This alternatively works for Nurse Joys and Officer Jennies.
  • On a related note; cubone are like salmon. They live their lives, travel several miles for a chance to mate, and then die once the eggs are laid/young are born. Which would explain how the baby cubone get their mother's skulls.
  • Jossed by the fact that males from other species can breed with them. Now, all-male species like Tauros and the Hitmon family, on the other hand...

The Kangaskhan you hatch is really the baby Kangaskhan.
Young Kangaskhans are extremely weak, and can barely function outside of their mothers' pouches for their first few years. Whenever one is hatch in captivity, a breeder will bring in a tamed Kangaskhan to act as a surrogate mother for you. That's the Kangaskhan you control in battle.
  • How does that Kangaskhan have Egg Moves, then?
  • The baby teaches them to the surrogate mother.
    • Which can only mean...

The "baby" in Kangaskan's pouch is actually the male of the species.
Like several invertebrates in real life, the male is significantly smaller and partially parasitic of the female. Presumably, Kangaskhan eggs exhibit gender-dimorphic twinning, and the male of each egg then departs to find a non-related newly hatched female to latch onto.

Kangaskhan's baby is her ovary.
  • It always bugged me how Kangaskhan is born with a baby. But then I realized... You know how female mammals are born with their ovaries? Kangaskhan's baby is her ovary, and she has a mind of her own. Kangaskhan has to protect her baby, or else she will become infertile. If Kangaskhan dies and the baby is still alive, then the baby becomes Cubone, and every baby that Cubone has is also Cubone, adapted to be born with the skull.

The reason Kangaskhan always has a baby is that they are twins!
It's just that while they are in the egg, one twin becomes dominant and gets most of the food, becoming the brawn, while the other gets less, becoming a parasite living off its stronger sibling, or a symbiotic creature acting as the brain.

Farfetch'd don't really use the leeks as swords.
People only tell the protagonist that Farfetch'd use leeks as swords for the same possible reason they say Pokemon eggs appear out of nowhere: Farfetch'd were stuffed with leeks when cooked pre-G1, and they just want to return the favor, in a way that's said to reduce fever. Which is extremely inappropriate for a ten-year-old to hear. None of them ever tried to "prepare Ash for broiling" because Pikachu would have killed them with electricity. Dead. (Alternately, they could spare the children, except those who actively hunt and cook Farfetch'd.)

Butterfree was originally supposed to be an evolution of Venonat.
Venonat. Butterfree. Also, look at Metapod and Venomoth. They seem to have much more in common as far as appearances go than Metapod and Butterfree or Venonat and Venomoth.

Tyrogue/Hitmonchan/Hitmonlee/Hitmontop and Smoochum/Jynx are the same species.
They are all humanoid, single-gender Pokemon, introduced in the first generation with pre-evolutions introduced later. Mr. Mime would have been a better counterpart to Jinx, but Mr. Mime comes in both genders.

All Makikarp used to be Relicanth.
In the Pokedex entry for Magikarp in Pokemon Leaf Green, it states that in the distant past, Magikarp used to be somewhat stronger. Relicanth is an ancient Pokemon. My theory is that a long, long time ago there was a great migration of Relicanth inland, they then slowly changed into Magikarp, losing their power in the process due to lack of use. Some Relicanth stayed in the deep ocean though, which is why you can find them still in ocean trenches.
  • Then would that mean that Gyarados is what happens when a Magikarp receives telepathic advice and strength from its powerful Relicanth ancestors, a la Avatar The Last Airbender, or something like that?

Cubone are actually baby Kangaskhan.
Think about it, it just makes too much sense. All Cubones have dead mothers. All Kangaskhans have children. Thus, when you consider the visual similarities, when a baby Kangaskhan's mother dies it makes sense that the child, loving its mother more dearly than any other Pokemon, as it is the only Pokemon to be carried in its mother's pouch, takes to wearing its mother's skull, which stunts its growth, and prevents it from growing into an adult Kangaskhan. Apparently, there are several diagrams that support this hypothesis.
  • One problem: the Cubones' skulls look nothing like Kangaskhan.
    • It only seems that way because Cubone is so much smaller than Kangaskhan, and the bottom part of the skull is missing. Otherwise, the bone structure is a pretty close fit.
      • Kangashkhan's snout is too broad and doesn't have horns.
  • You can breed and subsequently keep Marowak, so no, not all Cubones have dead mothers. The only one canonically confirmed to have a dead mother (there are various theories reconciling the breeding thing with the Mother's Skull) has a Marowak for a dead mother.
  • Plus there's the whole question of how simply putting a skull on one's head would change one's type, coloration, evolutionary chain, and stunt one's growth of the body instead of just the head. The whole theory's wrong, pretty much.
    • An item changing a Pokemon'd DNA and causing it to evolve? You're right, that's insane.... Steelix, Scizor, Politoed, Slowking, Magmortar, Electvire, Rhyperior...
      • You forgot Dusknoir!
      • Oh, ha ha. Very cute. Because "trade holding a special item specifically designed to cause evolution" is exactly the same as just putting a skull on your head. Troll harder, guys.
      • How about you troll harder? Anyways, ignoring that statement, my idea is that (for the in-universe explanation) Marowak is supposed to evolve into Kangashkhan...But stubbornly keep the skull on, which interferes with the evolution process, ergo their body refuses to change. There isn't really a way to shoot that one down, since we don't actually know for sure how a Pokemon's body works.
    • I feel that since Kangaskhan are only found in the Safari Zone and Cubone are only found in the Pokemon Tower, that some of those changes can be explained by the stress of the environment. While in the pouch baby Kanga/Cubone is living a normal life in the Safari Zone, having its mother hunt and fend for it, thus its type is Normal. After its mother dies, it has to travel to Lavender Town, and along the way, it takes to fending for itself, and surviving alone; the Ground-type is a pretty good choice for its life on the run. The coloration is quite simple, although purple as a baby, even as an adult Kangaskhan turn into roughly the same brown that Cubone do. Also, it could turn brown to blend in with the ground on the way to Lavender, to stay out of sight from Fearow and Pidgeotto. The growth can be attributed to malnutrition; no longer having its mother bring it freshly hunted food, it relies on finding berries and other scraps in the wild. Therefore, it doesn't grow as well. The evolutionary chain is tough to explain, but it can just be brought about by the different environment between the Safari Zone and the Pokemon Tower.
      • Except in Yellow Version, Cubone are found in the Safari Zone. Hmm...
      • Not to mention both Cubone and Kangaskhan are both found in the Rock Tunnel in Generation II...
  • One theory was that Kangaskhan was meant to evolve from Marowak, but it was decided against late in the development process, and removing all that code from the game would set it back for months. They moved that code into a numberless slot, creating the Missingno. glitch. Which is why some Missingno. will evolve into Kangaskhan.
    • That theory is also false. The whole thing is because of the index numbers of the various Pokemon- since there were 190 Pokemon planned for the first gen, but not all of them made it (this is actually true, confirmed via a fan asking Morimoto himself in person). This leftover data became the glitch Pokemon and due to the way the index numbers work (I suggest reading more on Bulbapedia), some gliches evolve into Kangaskhan. Cubone and Marowak are not, and have never been, related to Kangaskhan. Theory Jossed.
    • Nope, not if you take the "baby" Kangaskhan is actually an ovary guess above. The "baby" is just a body part with a mind of its own that undergoes an emergency evolution if it manages to survive the death of the main body, eventually enough of these came together to create the Cubone subspecies.

An evolution will be made for Pikachu that you can only get by refraining from evolving it into Raichu and instead leveling it to 100.
This is what Ash's Pikachu will become at the end of the series.
  • Of course, if you use a Light Ball, it only makes sense to do this. According to Serebii, the Max ATK and SP ATK of a Level 100 Pikachu with a hindering nature are 376 and 358, respectively. In contrast, a Level 100 Raichu with a beneficial nature tops out at 306 for both. You actually get weaker by evolving in this case, since the Light Ball only works for Pikachu.

Eevee are closely related to Mew, and were the first Pokemon to evolve.
That's why it has so many different forms. In the distant past, Eevee likely had forms for all the different Pokemon types; in modern times, only some of these forms have been 'rediscovered'.

Eevee originate from early attempts to clone Mew and/or unlock the secrets of evolution.
Their DNA is so irregular because they were an early result of all the testing and experimentation done with DNA from various types of Pokemon, including Mew itself. However, some scientists came to question what they were doing to these adorable little fluffballs and started Heel Face Turning, smuggling them out. (Bill himself could be one of these scientists, out to atone for his past crimes by using his talents to create helpful tools for trainers and breeding the species he created to make it more viable and ensure its survival as a species. Plus, they make adorable Morality Pets.)
  • This actually makes sense, in regains to all the new evolutions being found; as Eevee become exported to different regions they will adapt to their new surroundings with new Eeveelutions. And Bill does give you an Eevee in HG/SS.

Onix have a large buoyancy bladder in each segment of their bodies to aid with movement and decrease inertia.
And that's why they weigh less than water.

Mr. Mime was meant to be male-only when genders were implemented.
Specifically, the male-only counterpart to Jynx (Psychic types introduced in generation 1 only obtainable through in-game trades that would later get a pre-evolution. They also have similar base stat totals (differing by only 5 points post-gen 1, before that the totals matched and their speed and special only differed by 5 points), and similar Pokéathlon stats (Mr. Mime has one more point in base jump, but they both have the same possible max totals). However, someone messed up the coding with Mr. Mime, giving him an even 1:1 male:female ratio. Like Nidorina/Nidoqueen being unable to breed, they kept this in subsequent generations for the sake of continuity.
  • I don't think so. It's Japanese name (Barrierd) shows no sign of being male exclusive.
    • Not all gender-exclusive Pokemon have gendered names, though.

Diglett is a Hitmonlee submerged in the ground
A bit of a silly theory, but they do share some body similarities. An ovular, brown head which doubles as its entire body come to mind. Plus, it was mentioned in one of the Mystery Dungeon games that Diglett does indeed have feet. Sure, they don't look exactly alike, but hey, if that...thing on Slowbro's tail is a shellder, then anything goes.
  • An evolved Shelder that has venom, Diglett needs more help.

Jynx is a succubus.
It looks like its trying to seduce you, its moves are kissing-related (Attract, Lovely Kiss), and at the same time, it's rather creepy looking. This fits the description of a succubus, which has been said to be either very sexy or terrifying, as Jynx seems to fit between the two. This may also explain its Psychic typing: succubi and incubi invade people through dreams, so Jynx could use its psychic abilities to preform a literal Mind Rape. As for why they aren't fire types? Remember that, in the Divine Comedy, Satan was located in a frozen glacier.

Porygon are based off Poké Ball technology.
Poké Balls seem to have the ability to turn Pokémon into data. Porygon may originate from an attempt to reverse this: aka transfer the data in a Poké Ball into a Pokémon. Furthermore, this could go to explain why you find items disguised as Poké Balls: these were either a prototype for Porygon, or what Porygon was based on.

Arcanine IS fast, but is somewhat slower in landing attacks
Arcanine has a Base speed of 95. Still pretty fast. Apparently, hence Pokédex Entries, it might seem to have been rivaling Deoxys in speed all along. It can't control its own speed and needs to brake to change direction. And Braking will take long, unfortunately.

Reasons why Nidorina and Nidoqueen can't breed
Long story short, Female Nidoran can breed, but Nidorina and Nidoqueen are in the Undiscovered Egg Group and can't lay eggs (The entire evolution of their male counterparts can breed just fine though). So here, you list down all your reasons why among the whole evolution lines, only Female Nidoran can breed:
  • It was enforced where the programmers could only program Female Nidoran to lay Nidoran egg of either gender, but not Nidorina or Nidoqueen.
  • Nidoran are living in a Crapsack World, so to adept to their environments, Female Nidoran lays all the eggs, then evolves where it has a new role: Protecting the eggs it had laid.
  • Maybe their reproductive organs remain active as they evolve but the males can no longer access them due to the changes both lines go through. They never adapted to it since the base Nidoran form can still breed just fine.
  • A freak mutation resulted in the female line only able to mate in the immature stage
  • Or they could have gone through the Pokemon equivalent of Menopause.

Farfetch'd is a result of the programmers trolling the gamers.
A one-of-a kind Pokemon that doesn't evolve? Yeah, let's give it terrible stats and keep it that way forever. U mad, gamers?

Tangela was originally planned to be found in the grass above Pallet instead of beneith.
Think about it, it doesn't evolve (not for a few generations anyway), it's attacks are fairly weak, and it's found right next to the starter village. Sounds like it was being set up like Butterfree, something to help out players early on if they didn't pick Bulbasaur but would be replaced by better Grass types a few towns later. Either it being moved was an accident and they forgot players would need Surf to get to that area, or it was supposed to appear in both the above and below grass but they forgot to add the data, or they decided that they didn't need a crutch Grass type after all but couldn't remove it entirely.

Many species that we met first in Kanto are actually immigrant species.
I can't name any off the top of my head for sure, but this troper wouldn't consider it too implausible. If this is true, some of their further evolutions may perhaps have developed to adapt to certain changes in their region of receptions (I know that evolution doesn't happen that spontaneously IRL but this is just a wild guess, hence its being in this index).
  • This makes some sense. Just think of the Safari Zone. Safari mans exotic nature trip, so pokemon from the Safari Zone were shipped in.

The Charmander lines breathe through its tail
And their flames shows them exhaling constantly.

Zapdos was the energy source of the Power Plant.
Despite being a legendary with no history involving people, Zapdos is found slap dab in the middle of the Power Plant. While it could be possible Zapdos was attracted to the energy output and Electric Pokemon, it could be that Zapdos was used to power the plant. Many years ago, Zapdos was snagged by the owners of the plant, and its incredible electrical powers were used to power it. After the Plant was abandoned, Zapdos had become friends with its Pokemon co-workers, and decided to stay with them.

The Drowzee/Hypno family created the Abra/Kadabra/Alakazam family.
In the Johto region, Abra and Drowzee can both be found near Routes 34 and 35, the former of which the Day Care Center resides. Drowzee and Hypno both are said to eat dreams, with Hypno explicitly said to have eaten the dreams of humans. Abra sleep 18 hours a day, Drowzee found on Route 34 know Hypnosis, and Kadabra were once boys with extensive psychic powers who one day woke up to find that they had become Kadabras. It's possible that the Day Care Center was meant just as much for children as it was for Pokemon, only for a couple of unlucky children to play in the grass, come across Drowzee's, be put to sleep, have most of their dreams stolen, and turn into Abras. While they may be awake for 6 hours of the day,they might only be barely aware of their surroundings until they evolve into Kadabra. This also explains why Abra only naturally know Teleport, for self-preservation, and Teleport explains why they appear in different areas away from Drowzee or Day Care Centers. By G/S/C/HG/SS, the Day Care Center was reserved for Pokemon only.

What is Diglett?
Why do we never see any part of Diglett besides its head? Well, I'll tell you...but look at your own peril, lest you Go Mad from the Revelation. It's... an Eldritch Abomination! In particular, one that lives deep beneath the earth, and the part that springs up from the ground is merely a projection of its true form. So stop letting those horrid things screw your Wailords!
  • This would explain why Dugtrio is 3 Diglett, but unlike the other Pokemon that consist of multiple pre-evolved forms (Weezing, Magneton, Metang/Metagross), Diglett has nothing to do with magnetism or toxin-induced mutation...
  • HOLY SHIT!

Kangaskahn isn't born with a baby in it's pouch; that's a growth in the shape of a baby Kangaskahn.
We have never seen that baby leave it's pouch, and this is the best solution to the "how can it be born with a baby in it's pouch" conundrum.
  • It does in Pokemon Ranger if it uses Hyper Beam.

Related to the above: The baby kangaskhan is the actual pokemon, the "mother" is a giant "mech"
The actual pokemon you control is the "baby" knagaskhan, which drives a giant bio-mech that looks like an older pokemon. All moves are used through this bio-mech, and so in effect you're controlling the mech, but through the smaller pokemon.

If Arceus is God... Ratatta is Satan.
Perhaps you've thought that Gengar or Giratina would be the evil counterpart to Arceus, or Darkrai, or even those ghosts in Lavender Tower before getting the Silph Scope? No. Ratatta. Freaking. Ratatta. They're everywhere. They're hiding everywhere, waiting for you. You can never escape them, no matter how hard you try, they always come back eventually. Hiding everywhere, waiting for you, waiting for you to give in. You capture one, you raise it, it grows stronger, you give into power as it learns Hyper Fang, you give in to that lust for wrath and dominance.

Ratatta and Raticate were once electric types.
All the other rodents in the Pokemon world are electric types, so these probably were too, at one point.

    Ditto, Mew, and Mewtwo 
Ditto are made up of several de-evolved Pokemon combined.
Ditto can transform into all different Pokemon, and its colour implies a connection with Mew. This could be because Ditto is a anthropomorphic blob made up of several Pokemon that had their matter assimilated after battle. Thus, it can shapeshift into any form needed, but it cannot 'remember' a particular form, which thankfully prevents it from turning into a genetic mismatch of Pokemon (or tearing itself apart.) Nightmare Fuel ahoy.
  • So, Ditto are basically sentient lumps of LCL?
  • Don't be silly. Ditto are Mew that have lost their form over time. Hence why they can technically learn any move through Transform.
  • or they are stem cells

Ditto solve for everything.
Voltorb and Electrode are Ditto that transformed into Poke Ball shells and were unable to return to their normal shape after having the power source installed. The saplings you cut down only grow back when you aren't looking because they're troublemaking Ditto. This is also why there was a tree in the doorway of Lt. Surge's Gym. And Pokemon don't evolve: They just find a more efficient way to utilize their normal shape (that, or can only become certain things permanently after gaining enough mass or energy, hence the Pokefood but no Pokepoop dilemma). And Mew was a Ditto that just happened to figure out how to use all of its potential attacks in the same form. Ditto. Solve. For. Everything.
  • Whenever I play Pokemon Stadium, I always make sure to have a Ditto on my team.
  • Could they divide by zero?
    • Yes, but doing so turns them into a Missingno. if they're lucky.
    • But Pokemon do poop...

Ditto reproduce with other Pokemon by budding in a proper environment.
This environment is primarily found in the Day-Care Center areas, and may work for all Pokemon, or it may just be the trainer leaving them alone outside their Poke Balls (possibly in a situation where they are enclosed, so there is nothing else to do if they get bored). The Ditto duplicate the other Pokemon's DNA, and then bud off a Pokemon egg. Pokemon have three spaces for sex chromosomes (XYY or XXY, [[Rule34 XXX]] and YYY are presumable unviable), so that a Ditto can breed with either a male or female (at least in the later games).

All Pokemon are Ditto.
Think about it. They all understand each other, despite only being able to say their own names. No one has ever seen them breed, nor lay an egg. The reason they have egg groups in the first place is just because hey, some Ditto are picky. Different Pokemon exist and are continuing to be discovered because the Ditto keep thinking of new forms to take. Legendaries are just so awesomely powerful that no other Ditto dared to take the same form again.
  • Translation Convention on the speaking part. Humans only hear their name just like we can't understand animals.
    • Either way, they can understand each other, and humans can't.
  • The name speaking is only in the cartoon and spinoffs that take its lead, there are Pokemon that can speak human in the main series or otherwise have their own complex languages.

Arceus may have created the universe, but Ditto was the prime tool it used.
We know Ditto has the ability to transform into anything it sees. Therefore, it can transform into virtually anything in the accessible universe. Perhaps it originated as a simple, primeval mass of goo that Arceus used to mold everything. The planets, the trees, and even individual Pokemon. The original Ditto would only transform once, to become a single thing that could be used to contribute to something greater. When creation had finished, the Ditto had become sentient, and Arceus limited its power so it could only transform to what it saw and how often it could transform (so it would not challenge Arceus' power by simply transforming into it). Also, notice how in the Pokemon games, Ditto can't reproduce. That opens up a whole new idea on how Dittos form. Perhaps there's an endless supply of primordial goo becoming sentient Dittos.

Ditto was the second Pokemon ever made
Ignoring the recent universe-creating and alternate-universe crap and going back to Mew. Mew is the common ancestor of all Pokemon, right? Wouldn't it be much easier to create an entire... all those Pokemon if there was one that could become anything very early on? Plus they're both pink.
  • Also, they share a Shiny color (blue), and can both learn Transform.

He's more humanoid than Mew, seems to identify better with humans despite not liking them, and the effect on his personality can only be called Humans Are Bastards. Heck, his whole setup is chock full of hypocrisy for someone who wants to wipe out humanity, he's more comparable to a son of Giovanni. In fact, maybe they used Giovanni's DNA...

Plus, at the end of Mewtwo Returns, he's decided to hang out in a human city rather than with Pokemon, perhaps deciding he gets along better there. He's probably also fighting crime. I'd totally watch that show.

  • Apperantly, you have never read Pokémon Special. In it, we find out that the Cinnabar gym leader, Blane, was one of the head scientists in the Mewtwo project. We also find out that, because Mewtwo was unable to stabilize itself with the DNA it had, Blane had to add some of his own DNA into the mix. It works, but it also causes Blane to get some form of genetic mutation on his arm from the Mewtwo DNA, which, coincidentally, serves as a nice compass to tell you where Mewtwo is. Therefore, this is a proven fact, at least in one of the manga versions.
    • Woohoo, I'm a genius!

The main differences between Mewtwo and Mew aren't additions...
They're subtractions. Mew has in itself the DNA of every Pokémon, including Luvdisc, Farfetch'd, various pre-evolution traits that aren't expressed in their evolved forms, and various other weaknesses that, while improving its general versatility and allowing it to learn any TM or HM, reduce its overall power. So when it came time for the scientists to build a mon as powerful as the gods of space and time from the DNA of a somewhat less powerful Pokémon, they had to trim the fat: Luvdisc, Farfetch'd, Plusle and Minun, any Magikarp or Feebas DNA not expressed by Gyarados or Milotic, anything like that was removed from Mewtwo's genetic code. This made its DNA smaller and more manageable, but also somewhat unstable, forcing the introduction of certain human genes to make it strong and stable enough to survive the cloning process. That last part also made it almost human mentally.

Mewtwo is part Kadabra/Alakazam
I posted this earlier, but it seems to have disappeared. Firstly, Mewtwo looks a lot like Kadabra and Alakazam - bipedal, three-fingered hand, armoured-looking body, etc. Mewtwo's catlike face and super-long tail come from Mew, of course. Also, Kadabra and Alakazam are good at telekinesis, and I don't think I've ever seen Mew use telekinesis in the anime. Mewtwo's best magic is telekinesis, that's how he destroyed the lab and started the storm and pretty much all the really powerful things he did. Also, Mew doesn't seem nearly as smart as Mewtwo (although how much of that is being a Cloudcuckoolander is uncertain), and Alakazam is described in the Pokedex as having a ridiculously high IQ. Mewtwo is also much more serious and competitive than Mew, which could be due to trauma but could also be because Kadabra and Alakazam are somewhat serious and competitive. He can learn to use Miracle Eye against dark Pokemon, a move unavailable to Mew, but shared by Kadabra and Alakazam. And that's without bringing up manga Mewtwo and his giant spoon of death.
  • I've always thought that the reason for Mewtwo being so different from Mew was because he was more developed. When he was younger, he looked quite a bit more like Mew, but by the time he escaped, he was much larger. I'm guessing he was also much smarter and more powerful. Perhaps the scientists modified the gene that keeps Mew from growing after a certain point.
  • That idea wouldn't be too farfetched. After all, the whole point of creating Mewtwo was to create the most powerful Pokemon. It'd make sense that they'd take DNA from other Pokemon to include some more favourable traits to a weapon that they didn't believe Mew to have (such as the intelligence, understanding of the human psyche, willing to fight, and even maliciousness. And, as Alakazam is said to be the most smartest Pokemon, why wouldn't they decide to add in that intelligence to their nigh invincible weapon? In the Pokemon Special manga, Blane said he contributed his own DNA into the creation of Mewtwo, so it's very possible for other DNA from other beings to be put into the mix.

Part of Mewtwo's (and likely Mew's) brain is situated inside his tail.
Now before you start yelling "This makes no sense", hear me out. With that much mental power, you'd think his brain would be huge. Mewtwo's psychic powers are way too immense to be powered by merely that little head of his. His tail is huge and fat and sees to serve no purpose. Perhaps it actually contains his brain, or at least the psychic powers part of it if not the thinking part. Same goes for Mew, who is more or less his ancestor. Before you ask "What kind of animal has a brain inside its tail?": well, some dinosaurs did. For instance, a Stegosaurus had a brain too small to control the immense body. Therefore, an auxiliary nervous center was situated close to his tail. Well, something similar could happen in Mew and Mewtwo's cases; part of the brain would be situated in the tail to avoid the head growing WAAAAAY too large for the body.

  • Actually, the existence of a "second Brain", was only postulated to explain the existence of a large cavity that is now believed to have housed a glycogen body (basically a pocket of super-fat, although that's grossly oversimplifying it.)
  • Actually, Girafarig.
    • And then there's Espeon, which doesn't have a brain in its tail, but does use it to amplify and manipulate its psychic powers...
  • Hmm. Given that the tail is an extension of the spine, which in turn houses the spinal chord, which is effectively an extension of the brain, maybe it's plausible.
  • This would explain why their tails begin whipping around whenever they're about to unleash hell...
    • That's pretty good evidence against this WMG, actually. That sounds like a recipe for easy subdural hematoma.

Mewtwo's second neck is really his spinal cord.
Think about it. His head is naturally really effin' big to support that big psychic brain of his, so it needs some extra support. Unable to think up a better solution, Dr. Fuji and his scientists put Mewtwo's spinal cord in this second neck while making his original neck primarily muscle and bone for supporting the weight of his huge brain. There could still be room for his throat/airway in the first neck, but it would be mostly muscle and bone. Coincidentally, this would also make his second neck into an Achilles' Heel, giving a bit more depth to his otherwise indestructible reputation.
  • Really? I think it's his windpipe and/or a huge artery. His scrawny neck could never hold a windpipe and/or he needs a HUGE amount of blood heading towards his brain in order for all those psychic powers to work.
  • It's been officially stated that it is a bundle of nerves, basically serving as a second spinal cord.

Mewtwo is dying.
As an unfortunate side effect of Clone Degeneration, Mewtwo, as powerful as he is, has an unstable genetic code and a drastically shortened lifespan. Between RBY and GSC, Mewtwo dies as his organs fail, and his body decays until only the Berserk Gene is left as a memento of his existence. The remakes are more merciful: Mewtwo is still alive and well, but he's aware of his own mortality and impending death, which is why his HGSS sprite looks so sad.
[Note From Ed: Original entry said "As a flipside to his power, he was given an extremely short lifespan due to his Clone Degeneration. In the space between RBY and GSC, Mewtwo dies as his organs fail, and his body decays until only the Berserk Gene is left as a memento of [his] existence. The remakes are more merciful towards him: he's still alive and well, but he's perfectly aware of his own mortality, which is why his HGSS sprite looks so sad." All subsequent attempts matched the final entry.]

The first Mew only had one DNA sequence in its body... its own.
Think about it. Arceus's godhood aside, how could the first Mew contain the DNA of Pokemon that didn't exist yet? Occam's Razor: it didn't. But as time went on and more Pokemon emerged, succeeding generations of Mew became a living record of all the Pokemon that existed and had ever existed.
  • Though it's not impossible that the odd genetic code slipped in from the future via quantum. There's always quantum.
  • Mew made all Pokémon, using and modifying its own DNA, probably using its vast psychic powers. Mew doesn't have all Pokémon species' DNA; all Pokémon species have a little bit of Mew's DNA.
    • Mew hangs out with Dialga, who is a Time Lord. Palkia is possibly a Time Lord also. Either the Master or the Rani.
    • Or perhaps Palkia is the TARDIS (the spatial powers would explain how he can be bigger on the inside,) like one of the other theories suggests.
      • That brings a lot of Squick...

Mew was the Final Pokemon.
According to the Pokedex, Mew contains the DNA of every single Pokemon. This means one of two things.
  • Arceus extracted Mew's DNA to make all of the other Pokemon.
  • After Arceus created all the others, he created the perfect Pokemon using all of the other Pokemon's DNA, thus making Mew.
    • It's just the Poké-creationists that think that Arceus created all Pokémon: there is no official source stating that Arceus created everything, the only Word of God pertaining to Arceus is that *legends* claim that it created everything. The likelihood of those myths being true is remote however, in this troper's view.

Personally, I find the second far more likely.
  • Or Arceus created Mew, from whom all other Pokemon naturally evolved.
  • That would explain why Mew is the New Species Pokemon.

Ditto is the pre-evolution of Mew.
They're both the same colour(even when shiny), and both the only Pokemon who know Transform. Mew can learn just about any move, and Ditto can copy moves via Transform. Mew is described as being an ancestor of all Pokemon, while Ditto breeds with all non-legendary and non-baby Pokemon. Ditto is actually the primitive pre-evolution of Mew. The reason why you can't breed them from Mew/get Ditto to evolve is because Ditto can only evolve in time(and given they're probably indestructible, will be a while), and Mew refuse to breed for you.
  • Maybe ditto needs to collect DNA samples from hundreds of other pokemon species before it can maintain a stable form and learn moves permanently. That would explain hoe mew has the DNA sequences of all (or at least most) other pokemon and why mew are so rare. Breeding with other pokemon is one strategy for collecting the DNA if, say, a rampaging tauros won't sit still for a cheek swab.
  • Alternatively, Ditto is an "imperfect" form of Mew, similar to the relationship between Phione and Manaphy, but far more severe in that Ditto has only a few of Mew's abilities while Phione has most of Manaphy's.

Mew's stats will rise closer to Mewtwo's as time goes on
Mewtwo is just artificially aged. Team Rocket and Red think Mewtwo was a smashing success but consider that Mew is a fetus. Mew is the oldest creature in existence ever witnessed by humanity, the ancestor of all Pokemon, has some of the highest stats around and is not even close to being fully grown. It is going to grow stronger in future ages.

The reason it spends most of invisible and in hiding is because that's what's natural for free roaming infants to do. Real world circumstance does not overcome natural behavior, it is the same reason why Black Bears are timid, even though larger bear species are the only extant organisms left in their environment that are a direct threat to them.
  • Splicing together other Pokemon were an attempt at shortening the time it takes for Mew to mature, though this came with the downside of shrinking its movepool

Following the two above WMGs, Ditto, Mew and Mewtwo represent different stages of a living beings development.
Ditto represents the embryonic/zygote stage of a living being: it's effectively a mass of stem cells that have an undetermined fate. This would go to explain its Transform move-it is trying to decide what it will turn into. Mew represents the fetus. Finally, Mewtwo represents the adult form.

the Mew glitch was intentional
Maybe not intentional from Nintendo's side, but some programmer thought it was unfair to leave out Mew, except for Nintendo events, so he programmed in the glitch, so everyone could get it.

The reason Mew and Ditto are so similar are because...Mew has the DNA of every Pokemon
No, no. Hear me out. Since Mew has the DNA of every Pokemon, its normal and shiny forms are excused (there are a LOT of pink and blue Pokemon, even in shiny form). Mew's ability to transform is simply the same reason as it can learn the rest of the moves it knows-because it just has the DNA that allows it to. I bring this up because, unfortunately, the idea that Mew and Ditto are connected any more than that was jossed in an interview.

Dittos are failed clones of Mew
My idea is Ditto failed clone of Mew made by Team Rocket when trying to make Mew Two. They tried to make Mew Two from scratch but the sentient structure didn't hold and wound up being a sentient blob of cells. With it's net intelligence can reform its cells into whatever it sees, not because it has the DNA of every Pokemon.

Mewtwo is not a genetically modified Mew, but rather the evolved form of one
Notice that Mew and Ditto are the only Pokemon who can learn Transform. Notice that they also both have the same coloration and lack an evolutionary line.

First I am supposing that there is another natural process in the Pokemon world that would more properly be called "evolution" than the process that takes that name. For the sake of distinction, let us call this process p-evolution. P-evolution is the evolution with which we as inhabitants of the real world are familiar: a muse of design that appears sentient but is in fact an inevitable consequence of the fact that animals can reproduce to form offspring genetically dissimilar from the originals.

I am supposing that the ability to evolve, like all other qualities of a Pokemon, must have p-evolved over many generations and much time by growing necessity due to harsh environments.

I am supposing that Mew and Ditto, due to their own unique abilities and circumstances, managed to survive the harsh environment through its duration without the capacity to evolve, and so their capacity to evolve failed to p-evolve entirely and only partially exists. This is why they know the move Transform: the ability to transform is in fact the ability to temporarily and incompletely evolve into any other Pokemon.

I am supposing that when the Mew that Team Rocket captured was genetically improved, what specifically was improved was its evolution mechanism; the rudimentary genetic code it possessed that it was to use to evolve was filled out and completed in the most logical manner possible.

I am thus supposing, at last, that Mewtwo is the evolved form of Mew, but Mew cannot evolve into Mewtwo simply because Mew does not evolve. What Team Rocket did to create Mewtwo was take a Mew, supply it with the genetic code necessary to evolve, and evolve it.

Similarly I am sure that Team Rocket could do this with other Pokemon that do not evolve. I am curious as to what Gyaradostwo would look like. Probably unfathomably ferocious.

Mewtwo will always be created.
Despite being recently created, Mewtwo is often included with other legendaries in ancient depictions; such as Bill's door in the anime, and the constellations in Pokemon Snap. Likewise the Genesect movie shows that an independently created Mewtwo shows the same physical differences from Mew as the first. Mewtwo is a species of Pokemon that must exist, either through some sort of determinism or a Genetic Memory of one humanity encountered in the past. It's simply only capable of coming into being, as far as we know, via artificial means. Considering their psychic powers, they may even subconsciously influence their creators to ensure their own birth, albeit probably not remembering it themselves.
  • Perhaps Mewtwo is to Mew as Phione is to Manaphy, except with cloning.

    Missingno 
Missingno is Red's evil.
Missingno is created because of how they stored your information while the Old Man threw that Poke Ball. So, it can be said that it is created from Red, basically a clone. However, Missingno. does not look like him, and does some pretty strange stuff to Red's world. Red is, barring other WMGs, basically 100% good guy with absolutely no evil in him. How is this possible? It was split from him by a flaw in the universe. Missingno's own image is corrupted, and he corrupts everything he sees. He causes greed (the cloning of item #6), corruption (all the graphical glitches), torment (freezing your game) and even global genocide (destroying your save). Missingno is all of Red's evil turned into a living being. Much like in real life, he can control and even weaponize his evil (like many people doing evil things for fun and profit), but it can also consume and destroy him.

Missingno is a box that contains an alternate universe!!!
Missingno's sprite is a shrunken down version of the Kanto region's map, right? In other words, a very large place, compressed into a small container, like in that Futurama episode... Perhaps catching it causes the alternate world to open and fill the regular world, thusly causing everything to be all jumbled up and weird looking.

MissingNo.'s presence is screwing up time
MissingNo. has some connection to an alternate universe, as like above. MissingNo.'s presence is pulling the alternate universe into the same place as the normal one the game takes place in. When they align, time stops flowing properly, thus explaining why time doesn't pass after you become the new champion and the credits roll. MissingNo. was screwing things up even before you started your journey, explaining why there is no night: MissingNo. had already fucked up time enough that the world isn't really spinning. Catching the glitch screws with graphics and your hall of fame, and duplicates your 6th item... because you have just forced the worlds to blend somewhat, messing up space as well as time in ways the mind cannot properly comprehend.

  • Moral of this story: catching MissingNo. is a terrible, terrible idea.

MissingNo., 'M, and the other "glitch" Pokemon are Lovecraftian Eldritch Abominations.
Consider the following:
  • The "glitch" Pokemon generally appear as disturbing forms that cannot be properly perceived by humans (except for MissingNo., which occasionally appears in the equally-disturbing forms of a ghost or an extinct Pokemon's skeleton).
  • Reality behaves strangely around them. The most benign form of this is the Rare Candy Cheat, which duplicates one of the items held by the player when he or she encounters MissingNo. The more malevolent Charizard 'M transforms other Pokemon into copies of itself.
  • Trainers who encounter them tend to either go insane or die horribly. This one requires some explaining. Some "glitch" Pokemon cause the music or graphics of the game to distort, either in the overworld or in specific places like the Hall of Fame. Others corrupt the game so badly that they can crash the game or render the save file unplayable. Now, consider that everything in the game takes place from the POV of your character, the trainer. What does seeing and hearing things differently from everyone else sound like, if not insanity? And the game crashing, forcing you to restart from an earlier point in time, is similar to the way most other video games treat death - especially notable because it's impossible to die any other way in a Pokemon game. Finally, the corruption of a saved game file, which forever ends that character's journey by leaving him or her unable to interact with the world, is likewise the in-game equivalent of death or incurable, crippling insanity.
  • This is why people refer to this pokemon as Missingno (missing number). The scientists and researchers who study pokemon assign them their numbers. However, Missingno is such a terrifying creature who pulls at the sanity of whomever comes near it, that the researches have refused to acknowledge its existence. If we accept Missingno's existence, we are forced to question the existence of our own world. We then realize that life is filled with dark horrors which we can only understand as glitches in reality. And so, unable to accept this creature as real, nobody has given it a number. Its number is missing.

Thus, the various "glitch" Pokemon are reality-warping horrors whose very presence twists the world around them. In fact, given MissingNo.'s multiple different forms, it could be an incarnation of Nyarlathotep; after all, those who encounter MissingNo. and receive its item duplication boon are likely to chase after other "glitch" Pokemon as well, and even those who don't risk seriously destabilizing the Pokemon world by abusing their nigh-endless supply of Rare Candies and Master Balls. Both would fit perfectly with Nyarlathotep's goals of spreading chaos and insanity.
  • And if you catch it with only minor glitches? Is that some kind of Anti-Lovecraftian "win"?
    • Pssh, no, that's all part of the plan. Nyarlathotep wants you to think you successfully caught him with only minor sanity loss....
  • And thus, the Order of the Glitch are a budding cult wishing to bring these horrors into the world. WE MUST STOP THEM!
  • If the Glitch Pokemon are Eldritch Abominations... then what is in the Glitch egg? Is it so horrifying that the character's mind refuses to accept the being hatching out of it?
  • Given that some things happen differently in Fire Red/Leaf Green compared to the original RBY generation, it is conceivable that MISSINGNO. or its corrupted brethren have succeeded in destroying the world once. Arceus is credited as the creator of the universe by the events of Diamond/Pearl, but it is far more likely that he 'fixed' the world that was driven to warped madness by MISSINGNO and its ilk.
    • This would provide an in-story explanation for why there are fewer Glitch Pokemon in Generations II and onward.
    • Perhaps this is what the story of Lost Silver actually represents. Gold is dying and everything is trippy and dreamlike because reality is being destroyed. The presence of the Unown signify Arceus preparing the restoration.
    • Perhaps the volcanic eruption that destroyed Cinnabar was a coverup to prevent people from investigating MISSINGNO.?
      • More likely, MISSINGNO. is the Pokemon world's answer to Cthulhu, and prior to awakening, it rested just off the coast of Cinnabar Island. Mew's arrival prompted the reawakening of MISSINGNO., meaning that at the time of R/B/Y it had just awoken after thousands of untold eons of sleep. The eruption at Cinnabar is a result of MISSINGNO. razing the entire town in the wake of its fury. That means that MISSINGNO. and the other Eldritch Pokemon are still out there, roaming the Pokeverse and causing chaos wherever they go, but nobody's seen them in years... The reason that Red refuses to speak and dwells so far from Society is that he was driven mad by these monstrosities and cannot speak for the horror of what he saw. And even if he could speak, his words would all be in some mad, twisted Pokespeech that would drive even the most stalwart of Onix to insanity.
      • I want to personally thank everyone involved in the Cinnabar discussion here for finally giving me an explanation regarding Blaine (seriously, this is something that's really bothered me for years). It's mentioned somewhere in his gym in the first gen games (can't remember if the reference survived to the remakes) that once he was lost on a mountain and Moltres effectively saved his life by guiding him to a cave where he took shelter. We know that most legendaries (certainly the birds) seem to pretty much be demigods and when they get involved in a way like this, it tends to be with the basic purpose of making things happen the right way, and I've always wondered what Blaine was supposed to do/have done. Now I have my answer: He blew up Cinnabar to prevent/halt Missingno's awakening. It makes sense as it explains how everyone was able to evacuate in time and it fits with what goes on in the anime regarding his Pokémon and their attacks somehow encouraging volcanic activity. And considering that in the original Lovecraft story, a slow moving steamboat was enough to stop Cthulhu's rise, a volcano should certainly do the trick. Another possibility is that Blaine was an instrumental scientist in Mewtwo's creation (I don't know to what, if any, degree he's canonically involved with the project but I find it hard to believe that he wasn't) and Mewtwo subsequently crusades against the other abominations in order to preserve a world he loves (people may be bastards, but Mewtwo seems to like Pokemon more than Fuji ever could). I'm sure this could also be linked in with Cerulean Cave in some way but this addition is already too long.
      • If Missingno is Cthulhu, then who's M block?
  • Alternatively, Missingno is a whole 'nother Eldritch Abomination. It's the personification of Pokemon that shouldn't and never did exist.
  • Confirmed, they turned out to be the Entity.

No, no, no, Missingno is actually Arceus.
He's powerful enough to mess with reality, his Pokedex number is 493 (because there's only 151 in Gen 1), and every time you perform the glitch properly, you are actually performing a ritual to summon him.
  • Alternatively, MissingNo. is The Devil to Arceus's God. This is why he's at the opposite end of the Pokedex.
  • Or Missingno is Arceus' true form; it's just recently it decides to look more terrestial. In fact, the rest of the creation trio could be the old-school glitches in A Form You Are Comfortable With. Giratina is probably 'M or glitchy Charizard,and the deadlier glitches are why Giratina was banished in the first place

MissingNo. is a corrupted Pokemon Storage System
When you put a Pokemon in a Poke Ball, you are actually sending it to the Computer via a Wi-Fi system. The system is heavy used, so they only allow six sent up in the web, but when you don't have a Pokemon to send out, the Computer corrupts and grows sentience.

Missing No. are the living embodiment of the Pokeball's red laser thing
So when you catch a Pokemon, it gets zapped into the ball by a red laser. When you send it out again, it gets zapped back out by the same laser. Maybe whether a Pokeball is set to convert Pokemon to data or data to Pokemon is automatically toggled by a switch that's flipped every time the Pokeball is used.

So far, so good. So when you take a Pokeball to the computer to retrieve your Pokemon, what if you try to retrieve an empty slot? The computer thinks, "hur dur, he's trying to take something out so there must be something there." So the switch flips, but there's still nothing in the ball.

So suppose you then go out and throw your Pokeball. There's nothing in it, but it's set to convert data to Pokemon, i.e. send something out, not catch or call back something. So the laser bursts forth and piles up on the ground into a zappy blocky blob of light. For lack of any other information to affect, the Pokeball has converted its own conversion laser into a Pokemon.

This could explain Missing No.'s reality warping abilities to an extent. It converts whatever data it touches to living material, and whatever living material it touches to data.

Missingno and/or the Laboratory place is connected to the volcanic eruption on Cinnibar Island.
Did the scientists do something crazy? Did Mewtwo somehow set something off? (We notice that Red doesn't have Mewtwo in his party...) Was it necessary to drive off Missingno and prevent it from destroying Kanto? Did Blaine set off the volcano to save the world, even though it destroyed his Gym and the island in the process? (Gold says that the island was evacuated completely.) Or did Mewtwo go crazy because he can see Missingno's true form?
  • The Pokemon programmers mercilessly remove anything tangentially responsible for the major bugs. They blew up Cinnabar Island just in case a Missingno bug happened again - showing they didn't understand it when G/S came out, as the bug could also be executed in the water south of Pallet Town. They also removed the door from the Safari Zone building, when they simply couldn't fix the glitch city bugs related to the completed Safari Zone. Additionally, even the Old Man refuses to show you how he catches Pokemon in G/S.
    • There's some precedent for Nintendo stripping features because they caused problems, or were associated with problems. After Electric Soldier Porygon gave 700 kids seizures, Porygon never appeared in the anime again, even though Ash's Pikachu made the strobe-light effect that caused the seizures.

Missingno. is a failed first attempt at a manmade Pokemon.
Once upon a time, The Silph Co. worked with the lab on Cinnabar to create a Pokemon. Cinnabar was going for a more natural attempt, trying to bring extinct mons back to life (explaining its possible appearance as a Kabutops skeleton or Aerodactyl skeleton) and Silph wanted a technological attempt (explaining its common glitchy look). When the partnership went sour, Cinnabar eventually succeeded in bringing back extinct mons, as well as creating Mewtwo, while Silph used what they learned to create Porygon.
  • Meanwhile, a failed Silph Scope experiment created the ghost form.
  • Specifically...
    • There is actually a pretty good (albeit short) fanfic on deviantART that details this WMG.

MissingNo. is a damaged Porygon.
It's clearly some kind of digital being, and that doesn't leave many options.
  • Alternately, it may have been a failed prototype from an earlier attempt to make Porygon, that somehow ended up in the wild.
    • I've seen this before...
    • Porygon can exist in the wild because the world of Pokemon is in a video game to begin with. That's why looking at Missingno causes insanity. That's what happened to Red.
      • Wait, so the people who created/modified the Porygons were, to them, changing reality?
  • Conversely...

Porygon-Z is Missingno.
Combined with above theories that Missingno. is a glitched Porygon, and Porygon-Z seems to be a glitchy Porygon2, evolved with software from an unknown developer. Although this is a more "safe" one that doesn't cause insanity on sight.
  • Alternatively, the glitch that turns Porygon 2 into Porygon-Z is Missingno.

MissingNo is a benevolent PokéGod
. It duplicates the item in the sixth space as a sort of blessing. Everything inherently bad is just an accident.

Missingno is the Pokemon version of Lucifer
He defied Arceus and ended with his appearence and banned forever from polympus of Pokemon.

Missingno is actually Articuno's screwed up big brother.
The reason Seafoam Islands have two caves is because Arceus created them so they would become each brother's domain. However, Missingno wasn't happy with the deal (possibly because Articuno got the most intricate cave or something like that) and continuously defied Arceus. Arceus got pissed and sent Missingno into the Torn World, as well as stripping him of his legendary status, as punishment, where he became what he is today. And since he was no longer a legendary, he was also expelled from his domain, doomed to wander the world aimlessly. Except he didn't, and he now lives at Seafoam's coast, waiting to exact revenge on his little brother.

Reasons why I think they're brothers:
  • They live near each other.
  • They're both Flying-types (fine, one is "bird"), and Water and Ice respectively, which are elements that are closely related.
  • Their names are similar.

    • Uh, Seafoam Islands is one cave with two entrances. Just like most of the other caves in the series (the ones in which the point is to get from Point A to Point B rather than to find a Pokemon or item, anyways.)

Extrapolating on the previous guess, Missingno was originally called Aquatro, the fourth legendary bird.
All of the Legendary Birds have names that begin with a word related to their primary type and end with their number in Spanish. Aquatro was a Water/Flying type, but because it was cruel and sadistic, it had his type warped by Arceus (Flying, which is a standard type for a Pokemon, became the unique type Bird), and it was stripped of its number, becoming Missingno.
  • Actually, Aquatro was the working title for Lugia.

MissingNo. is the original, pre-Continuity Reboot version of Deoxys
Part of the inspiration for this came from this page on the "Serebii" fansite, but the more one thinks of it, the more it all fits together. That page seems to be broken and glitchy, without data where data should be, but its very presence (as of Generation V, there are only 649 Pokémon) is data where data shouldn't be. Like a certain glitch Pokémon found only in Generation I. Take a closer look at the stats, though: its Attack-forme Deoxys' data. Now, I'd not be so stupid as to base a theory entirely on one page from a fansite, even if that fansite's had some accurate info in the past about the then-upcoming Generation V. But take a look at the Bulbapedia page for Missingno. itself too, with official stats on the Eldritch Abomination itself. In the original R/B, Missingno. had four forms, like Deoxys has. It only had one form in Yellow, a form only accessible in Yellow, just like how Deoxys' forme in its debut generation was based on the game in which it existed. Missingno's stats in R/B? Incredibly high Attack, shitty defenses. This was before Special was split into Special Attack and Special Defense, so we can assume that its Special would have become its Special Defense in later generations if it existed then. Similar enough to Deoxys in N-forme or A-forme, though the Speed was definitely changed (in addition to being Glass Cannons, Normal- and Attack-forme Deoxys have, quite literally, more Speed than Arceus) in the switch from Gen1/2 continuity to Gen3/4/5 continuity. And then there's that Deoxys' earthly home in FR/LG/E was Birth Island in the Sevii Islands, an island south of the continental part of Kanto just as Cinnabar was.
  • As for what might have happened? Well, Missingno / Deoxys was too much trouble in the old continuity. The then-existing incarnation of what we now call Arceus needed to change things FAST or all of Creation would have gone down the tubes. That volcanic explosion to destroy Missingno's habitat would only be a temporary solution. So Arceus reset everything, and made it that instead of Missingno. being a Bird/Normal-type Eldritch Abomination in Kanto, it was a Psychic-type alien from outer space, which made it less dangerous as now it followed the same set of rules as the rest of creation.

Missingno. is the Weedle.
It's like in Chocobo's Dungeon 2. Early in the game, you chase a Guz, a very weak enemy, out of a crystal chamber. But you get thrown out, and the Guz stays behind and touches the crystal. It wishes for power. Over time, it became an Eldritch Abomination, tearing apart time and space.

The same thing happened to that Weedle.

Missingno. is the result of humans eating Rare Candies.
One day, an 'ingame' human trainer called No decided to see what a prototype Rare Candy really tasted like, so he tested it out on himself while surfing at Cinnabar Island. The scientists had cloned the Rare-Candies beforehand but it turned out THIS Rare Candy has special properties unfortunately for No, so the Candy reacted with the saliva of the trainer No, causing a massive implosion. Horrified, the trainer's data was scattered and merged into a weird consummated mass that resembled a Pokemon- and the trainer No was considered 'missing'. That is why humans don't eat Rare Candies anymore. The new Pokemon called Missingno still wanders around calling his name...
One more really big freaking theory on MissingNo.
MissingNo was a prototype of Mewtwo which escaped containment. This explains why it's found near Cinnabar Island. The prototype split its consciousness into two entities: MissingNo and OLD MAN. When Red met MissingNo, MissingNo tried to possess him, but failed due to Red's determination to become the ultimate trainer. However, prolonged attempts by MissingNo caused Red to lose the ability to speak. After his defeat at Mt. Silver, Red became fully possessed by MissingNo.

MissingNo wanted revenge against the scientists who created it, so it gave Red supernatural powers and used him to wreck the Abandoned Ship, which had all but one of the scientists on it. The final scientist had gotten a new job at the Old Chateau, which had been an inn originally (Thus, the old Gateau). The scientist worked as a butler, and his daughter had a permenant room upstairs.

MissingNo used Red to kill the scientist and his daughter, and then decided to kill everyone else at the inn. However, Red broke free of MissingNo's control and poisoned himself, attempting to destroy MissingNo. MissingNo regained control and tried to take an antidote, but a brave guest at the inn grabbed it and threw it in the trash. This turned MissingNo into a ghost, which traumatized the guest (a little girl).

The little girl escaped, but she suffered near-insanity for the rest of her life. She stayed in Lavender Town and asked everyone who passed by if they believed in ghosts, all while seeing MissingNo's white hand on their shoulder.

MissingNo was trapped in the Old Chateau by Red, using the powers MissingNo had given him. MissingNo was contained in the statues, the painting, and the TV.

After many years, MissingNo realized what it had done and felt very sorry. When the player in D/P/P showed up, MissingNo transferred its consciousness into the TV and took physical form, letting the player capture it. Therefore: Rotom is actually MissingNo.

Smaller theories:
  • After dying from the poison, Red was ressurected by Giratina and became Steven Stone.
  • When MissingNo was trapped in the Old Chateau, the OLD MAN was trapped in the Safari Zone and became glitch city.
  • When MissingNo became Rotom, The OLD MAN became the Unown in the Ruins of Alph.
  • Before anyone points out that there were Unown in the ruins of Alph before Red lost at Mt. Silver, MissingNo and OLD MAN can time travel.

All right, done. Discuss.

MissingNo is a race of Pokemon native to the Distortion World
The disturbance caused by Cyrus summoning Dialga and Palkia caused rifts across time and space. It ruptured the fabric of reality near Cinnabar Island and allowed a MissingNo to escape. As it is largely made up of anti-matter, it damages reality around it. The reason you don't see any when you visit the Distortion World in Platinum is because they were scared away by you and Cyrus - they've never seen a human before and therefore were frightened.

Missingno. is something that should never have existed in the first place, according to the Head Programmer (they couldn't program just 150 Pokemon, they had to go with 300), thus it's, in a way, rejected, and sealed away by its god, and can't be gotten rid of due to the way the world works. However, when its summoning ritual is completed and it's captured, for even a fleeting measure of acceptance, and maybe even "love," it acts like a Pokemon, and it's ecstatic to be acknowledged, let alone cared for and played with. That's the source of it's corruption; it's too excited to not let its should-not-be-ness shine through.

Missingno. is a Yandere.
It wrecks your game to try and escape, and when it does, it corrupts living people just to live with you.

    Kanto Player Character-Related Guesses 
Red is Hot-Blooded, not The Stoic.
He's just quiet in GSC/HGSS due to a Heroic BSOD of some sort. All of his counterparts are Hot-Blooded and goofy. He's Blue's rival and best friend too, so you can presume that they have at least similar personalities unless it's an "opposites attract" sort of situation. Blue once called him a "chatty gossip" in FRLG, too. This is supported by an old "How To Make Origami" book with a comic drawn by Ken Sugimori himself. Red is shown to get flustered easily, loud, and have a hot blooded temperament. We can also presume that Leaf is quite eccentric. We can also guess from his canon actions, as described in the manuals of RGBY, that he is curious and willing.

Leaf and Red are twins.
You never see Red's father aside from a vague line about him liking something. It sounds like they're separated. Red's mom got him and the father got Leaf. They do look more similar then the other psuedo characters.
  • Alternately...

Leaf and Red are Opposite Sex Clones.
In one universe, the player's mother had a boy. In another, she had a girl. Simple as that. It's why we've never see Leaf after her introduction-Yellow is generally considered canon, and Leaf is part of Fire Red/Leaf Green.
  • FRLG is canon, not Yellow. Even in G1 and G2, Red was the canon game.

Red and Leaf are siblings and their parents are divorced.
Which is why your father is only mentioned once and you never see your counterpart. When you start the game, you're choosing who gets to live with the mother. Though, even if Red is sent away to his father (who could live in any of the other regions - probably Johto, though) he still tries, and succeeds if Blue/Green is to be believed, to become a Pokemon master. It is possible that Leaf and Red would continue to fight each other again and again for the title, or possibly even take turn being the Kanto champion, so that the other could go on vacation or something.
  • Wasn't that what I said a few WMG's above?

Leaf was kicked out of Gen 1 because she lacked a Nice Hat.
It doesn't matter if she wears a nice Little Black Dress, or she has a cute Idiot Hair-like thing. No hat? You're no protagonist of the main series!

When Leaf next returns, her hair will be down.
It'll be post-FRLG. Compare Red's hair in FRLG to his hair in HGSS; The bangs are down. The same applied for the original games.

That's not Red on Mt. Silver in HGSS, it's Leaf.
Red and Leaf look the same, and they may even be siblings. They're gender bent versions of each other, unlike other protagonists (even Dawn and Lucas look quite different). Just put Red's hat on Leaf, with most of her hair in it, and put on Red's clothing and they're identical twins. Red is also completely silent, which goes against the hints to his personality pre-timeskip.

Leaf is Red's equivalent of Ashley.
A 10~11 year old boy can pass up as a girl and sell it without much difficulty. It explains why the two never meet, as well as why we don't see her in HGSS, because his crossdressing isn't convincing anymore. This, of course, doesn't apply to the manga.
  • Special!Red =/= Game!Red.

That version of Red that the fandom sees is what in-series people think he looks like.
People that don't know him, that is. He's full of mystery.

Red's canon starter is Pikachu.
How else could he get the three Kanto starters without trading? By starting with Pokemon Yellow and getting a Pikachu, which you can't evolve in your game.
  • There could be many reasons, actually.
    • Are you suggesting that Red used a glitch? Why would he not evolve Pikachu, then? Evolved forms are usually stronger... And that's for the original versions. The remakes on the GBA lack Missingno. and its fellow glitches, and I'm pretty sure HeartGold and SoulSilver follow from them, or more to the point, from a never-planned, never-released "third version" that would have been to Yellow what FireRed and LeafGreen were to Red and Blue. However, we also don't have evidence that he didn't trade to get them either.
      • Maybe his Pikachu doesn't wish to evolve. Or he just likes it that way.
      • Who wants a weak Mighty Glacier when you can have a Lightning Bruiser courtesy of a Light Ball and some Carbos or Iron?
      • Maybe after Blue got over being a Jerk Ass they decided to trade. Red could have gotten the last starter from Prof. Oak OR if Leaf's existence is canon they could have traded as well.
    • You could get the starters from Pokemon Stadium by beating the Elite Four at Gym Leader Castle (and you could get Omanyte, Kabuto, Eevee, Hitmonchan, and Hitmonlee the same way.)
    • Um... This is probably Jossed by the fact that, in G/S/C and their remakes, Blue uses his Red/Blue team rather than his Yellow team. They were trying to avoid giving Red and Blue canon starters.

"Red" does not exist.
Inspired by the above. He's a persona of Leaf. Leaf goes into drag, probably since there are few female trainers at that time or such. Why doesn't Blue know? Either he does (maybe that's related to his Jerk Ass behavior toward him/her), or he thought Leaf was a boy for their entire friendship.. Or she made an excuse about her going away or something, and her non-existant brother coming over.

Red's surname is Tajiri.
Hey, if his anime counterpart can have Satoshi Tajiri's given name...

Red is hard of seeing.
This may explain why he mistook a Voltorb/Electrode for a Pokeball item, despite it being much larger than one.
Red is Blue and Blue is Red and vice versa.
Ever notice that the protagonists in both games are default named after the color of their gaming cartridges in the original Red and Blue? That's because it's not telling the same story. Red sees Blue as a douchebag rival that's out to beat him, whilst Blue sees it as the other way around. It looks like the story is being told twice but it's really told in Red's POV in the red version and Blue's POV in the Blue version. The series was being told, "Rashomon"-Style until Yellow broke it by incorporating events from the Anime.

    Your Rival 
Blue joined Team Rocket at Nugget Bridge.
Think about it. He's in Cerulean City, coinciding with the Rockets showing up there. He's in Pokémon Tower when Rockets are there. And then who should show up at Silph Co.? Blue. Blue shows up at Silph. And then, right after you beat Giovanni for the last time in Viridian, and you head out to Victory Road, he shows up yet again, and this time with a Rhydon. Who else uses members of the Rhydon family? Oh, yeah, that guy who you just beat and is head of Team Rocket.
  • Also, the Viridian Gym was under control of Giovanni. In Giovanni's departure and absence, who else better to take over the gym after, than a Rocket associate? Blue.
  • Notice his dialogue in Silph "So you are ready to face Rocket Boss." This indicates that he may have served as Giovanni's dragon or something and was guarding him from others. He does seem to just be sitting there in the last room before Giovanni without doing anything.

You killed your rival's Raticate on the S.S. Anne.
In the game, you encounter and battle your rival in Lavender Town. He asks something along the lines of whether you're there because one of your Pokemon has died. When you battle him, you find that he no longer has the Raticate he had possessed in earlier battles. Before this battle, you had fought your rival on the S.S. Anne, and his Raticate, having taken severe damage, was unable to make it to a Pokemon center after the battle due to the crowding on the ship. The real reason your rival is in Lavender Town, in the Pokemon Tower, is to lay down his dead Pokemon.

The reason why Blue no longer has his Raticate
It's generally accepted that it died somehow. Some say Red killed it (see above WMG) while others say it was mortally wounded in a battle. Here's the real reason.

Remember how Blue's Raticate was level 16, even though it evolves at level 20? A mysterious stranger gave Blue a special kind of Rare Candy that made Pokemon evolve quicker. Little did Blue know, this stranger was from Team Rocket and the "Rare Candy" was really one of their ideas to induce evolution. They were handing them out to various trainers to test the results and hopefully recruit new members when the trainers saw how well it worked. Ever trainer who used it ended up having the Pokemon they used it on die, which forced Team Rocket's scientists to go to their next ideas.

As for Blue's Pidgeotto, it just grew up faster than others of its species.
  • Or he could have replaced his Pidgey with a different one. Pidgeotto is a 1% chance encounter in Viridian Forest in Yellow, and is after the Route 22 battle but before the Cerulean one. Doesn't explain the other versions, but still.

Assuming Blue was telling the truth about having caught a Cubone, it was released or put in a box for having harmed his Raticate before being caught.
This handily explains why he has only five spaces despite supposedly owning two Pokemon not in his team; The Raticate was taking a well-deserved break (or feeding the soil in the Pokemon Tower), and the Cubone was either sent off or left in a box because Blue couldn't stand to treat it with even his idea of respect after it harmed his Raticate beyond the normal limits of battling. My guesses for what it did: Intentionally landed a strong attack on Raticate after it had already fainted, before Blue could recall it, or killed it. Alternately, wanted to leave a space open for the Marowak/Cubone and/or was lying about catching a Cubone in the first place, but the former seems a bit roundabout.

Blue lied about catching a Cubone, and had a spot open on his team in Lavender Town because he didn't want to bother going back to the PC on his way out of town from catching a Marowak.
But I may just think that because of facotrs outliked in the above guess, and because {=Cubone/Marowak=} are one of the breeds of Pokemon that I like to raise through their evolutions instead of catching one of each (when I intend to use them, and aren't just catching them for the Pokedex or for breeding).

Blue just put his Raticate in the box.
It's not like you're the only person in the entire game who can do that. The PC is in every Pokemon Center, it's obviously used by other people.

Blue's canon starter is Umbreon.
Based on the anime.
  • Sorry, but Gary Oak's starter was Squirtle.

Nothing unusual happened in the Lavender Tower in regards to Blue's team.
Blue dumped his Raticate in the PC when he decided to catch Marrowack. When he couldn't find one he caught a Cubone instead but it fainted before Blue battled you, which is why it seems he's only got five Pokémon. Afterward he either got sick of training Cubone up or found Marrowack to be unimpressive and dumped it in the PC as well. Remember, Blue didn't bond with his Pokémon so he only cares if they're powerful/useful.

    Other Character Guesses 
Agatha is Blue's grandmother.
Both she and Professor Oak were rivals as children, and seem to be on good terms. It's possible that they used to date/were married, but divorced some time ago. Blue must've inherited some of her jerkassery.
  • Alternately, she's Blue's grandma on the opposite side of the family, for those who don't like Foe Yay. Plus, the idea of Agatha and Oak being rivals, and their kids eventually getting married, would be some rather funny Irony.

Agatha is Morty's grandmother.
Well, they´re both blond, and their signature mon is Gengar. Theres got to be some connection. Really, whats wrong with Game Freak? Agatha is the character you see less in the Pokemon series.

Lt. Surge is an ex-POW from World War II.
Sometime during the final stages of the war, Lt. Surge was captured by the Japanese and placed behind an electronic barrier in a war prison in Vermillion City. Once Japan surrendered, Lt. Surge was freed and was granted permission by the U.S. Military to turn his old war prison into a Pokemon Gym, with him as its leader and his cellmates as its trainers.

Professor Oak has Alzheimer's.
He's constantly forgetting things that you'd think he would remember, like, y'know, his grandson's name. Now he's tragic instead of hilariously forgetful!

Oak's last three Pokemon (in the games) are his pets.
That's why they're level 5. He never used them for fighting.

Erika and Sabrina have some interesting gym leader ties.
Why the hell does Erika's Pokémon have so many damn Psychic moves?
  • Are those yuri goggles on too tight on your part, troper?
    • Well, in later editions, she does gain some Pokémon with a fair few Psychic moves...
  • ...Good gym leader relations indeed.
  • Erika's Pokémon only really get the psychic moves in Pokemon Stadium 2, mind.
    • A long relationship then, maybe?
      • You're one hopeful troper.
      • To be fair, in the first battle with Sabrina in that same game, she does have a Wigglytuff with a Grass-move. Maybe Erika was more open to Sabrina's... tips but maybe not as much vice versa, so it'd seem.
      • This troper in particular think that the above point just makes a very subtle yet rather in character relationship between the two.
  • Hold your horses, there's something along those lines in Pokemon Stadium 1 as well. The ratio of Grass to Psychic moves (though few in number anyway) of the two is a little bit more balanced.
    • I'm calling that the part of the relationship where Sabrina is more of a generous soul before either going back into her shell after people start talking about them or Sabrina is getting cold feet.
      • I sure hope it's a case of her being Tsundere, but wouldn't that be before Erika "cracks her shell" so to speak?
    • Jeez, you shippers will read into anything wont you?
      • You say that like it's a bad thing!
      • Call it "Rule 35." "If it exists, it WILL be used to ship. Eventually."
      • Actually, Rule 35 reads: "If no porn is found of it, it will be made." Established, but pretty close actually...

Erika's a lesbian.
She has an all girl gym, surrounded by flowers, she's a bit touchy-feely with Jasmine at times (who in her own right can be seen as lesbian), and she gives out a rainbow badge.

Erika is narcoleptic.
She could be affected by her Pokemon, but no one else in her gym is.

Bruno and Brock are related.
Look at Bruno: he has a very similar hair style to Brock, and generally looks quite familiar to Brock. Sure, Brock's Ambiguously Brown, but that's either due to him being of a mixed-race or being really tanned. This also goes to explain why one of Bruno's Pokemon is Onix. Perhaps Bruno is Brock's father, and former leader of the Pewter City Gym.
  • Jossed by the anime.
    • Anime canon does not equal game canon, and anime-Brock's dad was a whole new character anyway. It's still possible in the games.

The people that are guarding Saffron City are working for Team Rocket.
They act rude to people and complain about being thirsty to deter people from coming through and interfering with Silph and to make it seam less suspicious that they are blocking off a road for no reason. For further evidence of this, the guards east of Vermillion let you pass even though the the road is blocked by a Snorlax, while the Saffron Guards block off a perfectly good path. Maybe giving one of them a drink is like a secret signal. When you give one of them a drink, he will mention sharing the drink but never leave his post. That is just plain weird anyway, but it could have been code for saying "access granted", more or less.

The Saffron Guards' superiors are working for Team Rocket, and they themselves are looking for excuses to ignore orders.
When you give them a drink, they finally notice that you have a competent number of badges, and start thinking that you can do some good.

About Sabrina disliking fighting
Can't remember whether she said that in this gen or the next one, but here's my opinion:
  • Considering how overpowered Psychic types were back in Gen I, it's possible that she doesn't like to fight her opponents, she likes to ''curb-stomp them. So, maybe it's not so much battles she dislikes as ones where she actually has to earn her win.
Team Rocket's fall was a bad thing.
It caused an evil team power vacuum, from which sprung other teams.

Sabrina might get an Espurr/Meowjestic in later games
Well she and the Espurr line have a lot in common. (powerful psychic powers, and maybe the desire to restrain them so that they would not harm people.) I'm not sure how this applies to the gym match, but she will defintly have a Meowjestic in the rematches and possible Johto remakes)

Prof. Oak follows the player around
How else is he able to tell the player not to ride his bike indoors or not to fish on the ground? He's always hiding just offscreen.

Red and Blue's rivalry is the subject of an underground gambling establishment in Pallet Town.
Red and Blue were actually good friends as children, until Professor Oak started instigating their rivalry and conditioning them to become enemies, knowing he could take bets on which will make it farther once they get their Pokemon licenses.

    Plot and Setting Guesses 
The Kanto Pokemon League is in a underhanded secret deal with Team Rocket.
Think about it, while Giovanni is the leader of Team Rocket he is also the leader of the Viridian City Gym. So either Giovanni somehow deceived the Kanto Pokemon League and the Kanto Pokemon League has no idea that Giovanni is also Team Rocket's leader. Or there is some corruption going on within the Kanto Pokemon League.
  • Well, if you consider that in Team Rocket circumstances, only people that presented a serious threat to the organization would be able to battle Giovanni as the boss of Team Rocket in the first place, so it seems that very few people would know about that, and Red/Leaf and possibly Blue and Professor Oak would be the only ones outside of Team Rocket (knowing that the Rocket Boss is named Giovanni doesn't automatically mean it is the same Giovanni that runs the gym, for those that do know his indentity). And Giovanni's pretty secretive and selective about who gets in his gym, you need to have 7 badges and the like, and even then, I believe the door is locked most of the time. So the chances of someone who has battled the final gym and also posed a serious enough threat to TR to battle their boss existing is slim, so it's basically limited to the protagonist (and possibly the rival, as there was probably a different leader if/when Oak challenged it). Of course, the whole secret came out after Red defeated him, but by then he was gone and it was a moot point.
  • Given that Team Rocket is supposed to be the family friendly version of the Yakuza/Mafia, it's trivially easy to come up with something grimdark about how they came to power.

Silph Co. is actually a rival gang for Team Rocket.
Oh, sure, they say they produce Poke Balls and such, but a place like that would obviously give tours to increase revenue. Unless, of course, they had a sinister secret.... This also explains why TR targeted Silph and stole a Silph Scope, rather than just hiring one of the Channelers who wander Pokemon Tower and obviously can see ghosts. Besides, where do you ever see any evidence that Silph is a legitimate organization?

Team Rocket's really the "Good Guy Group".
Unbeknownst to members outside of Team Rocket, all Pokemon emit small nuclear waves that, if ignored, could screw up the environment, machines, and even a human's mind and body. The rarer and more powerful Pokemon, the larger and more powerful the waves. Team Rocket is trying to find and capture rare Pokemon to prevent this environmental disaster from happening. They constantly say they're the "Bad Guys" because they realize that even if they explained the situation, no one would believe them and see them as the "Bad Guys" anyway, so why not have a little fun and declare it to the world? This explains why they're so hammy. I mean, really, nobody is that over-dramatic naturally.
  • Remember that those cute little monsters they're catching are cute little MONSTERS. Monsters that attack humans who wander into tall grass. Oak flips out at the thought of some poor defenseless little child taking a short walk to the neighboring town. And rather than giving the kid a taser or a whistle or something, the kid gets a tamed monster for their only defense. The only way to protect yourself from these random encounters is to have your own monster, which can only be obtained by having someone who already has a monster give you one. Or sell you one. Team Rocket is trying to equip mankind in order to fend off the horrendous beasts waiting just outside town. Constantly waiting, constantly watching...
  • In the first games, Team Rocket run a fairly ordinary casino, completely open for everyone to see. Their leader runs a Pokémon Gym. When the player breaks into their HQ under the casino, they naturally try to stop him. Ok, they steal the Master Ball, which it turns out is highly useful in capturing Mewtwo, a dangerous lab experiment gone awry. They're trying to capture all legendary Pokémon to 'protect the world from devastation'. That is, until you disrupt their organisation. Nice Job Breaking It, Hero.
    • Except the "protect the world from devastation" is English dub anime only, and Team Rocket robs people and actually killed Pokemon.

The area between Cerulean Cave and the Power Plant is somehow important to Kanto and Johto Legendaries.
Mewtwo in Cerulean Cave, the Mew Glitch being easiest to activate (and activated earliest) with a Trainer just outside the cave, Suicune running there in HG/SS, all the way out to Zapdos in (or outside) the Power Plant... Clearly, there's a reason for these Legendary Pokémon to be in this area, especially Legendary Pokémon from Generations 1 and 2 when there weren't that many Legendaries in the first place.

If there was a war that killed most of the previous male generation, then Lavender Town was a death camp/mass grave site/war memorial.
I read a theory that most of the missing middle aged characters were killed in a horrific war in the Kanto region in Red and Blue. I decided to add onto this WMG.

Lavender Town was formerly a normal village, until an undefined side (let's call them the Reds) came to the town. They were similar to Nazis in that they just went golly over psychotic torture and murder. They took the town, and recruited the occupants. They made two sides, the Normal Town and the Death Camp. The Reds sent Prisoners of War from the other side (the Blues) to their death here, along with Pokemon. They used horrifying experiments on both the Pokemon and the POWs, usually splicing the Pokemon and POWs together. The war was coming to an end when the Reds' last station was Lavender Town. Fearing punishment for their henious deeds, they killed the abominations that were now the POWs (they had long since spliced them all together with Pokemon) and buried them in one mass grave which would be under the Pokemon Tower. The Blues were also winding down, they had wasted all but one platoon trying to get to Lavender Town. Most of the platoon was killed by the defending force of Reds, but it also worked vice versa. There were only two soldiers left. The Red killed himself in fear of torture for the horrifying deeds they had done. The Blue killed himself because he had lost all his friends, and had nothing to live for.

When the dust cleared, the women and children rebuilt Lavender Town as a memorial for the war and a graveyard. All they needed was a sign in front of the Pokemon Tower saying "Never Again." Plus, the music does really sound like it should be playing in the memorial for Auschwitz.

After screwing up with Mewtwo, Team Rocket went to work on making Missingno. more powerful in Yellow.
First of all, the creation of Mewtwo would have supplied Team Rocket with a vast amount of knowledge on how to engineer Pokemon (and why you shouldn't underestimate said Pokemon). They could have tried again with the experience Mewtwo had given them; since Missingno is so close to the mansion where Team Rocket experimented on Mewtwo, they probably knew about it.

Second of all, it would explain Missingno's increase in power between Red/Blue and Yellow. (In Red/Blue, Missingno. just makes you go insane. In Yellow, he kills you).

Finally, it explains why Missingno vanished in Yellow; Team Rocket has it, so it's not there unless you try to import it in.

The Marsh and Soul Badges are not mixed up.
Instead, Sabrina and Koga inherited them from previous gyms, of different types.
  • Saffron originally had the Poison type gym, until the Fighting type group ousted them and changed the gym's specialist type. When Sabrina beat the Dojo leader and robbed it of its official status, she took the Marsh Badge for her own gym.
  • Fuchsia had a Ghost-type gym, run by Agatha. With few Ghost types in Kanto and even fewer trainers able and/or willing to work with them, and what Ghosts are present having ties to the Poison type, the gym shifted to training Poison types after the previous Poison type gym became the Fighting Dojo, although the leader still used ghosts (This also being the reason Agatha has a Golbat and Arbok). When Agatha was promoted to the Elite Four, Koga took over, but as he only used Poison types the Soul Badge lost it's meaning altogether.
    • Koga used only poison types, but a few of his trainers use Psychic types. His Gym is just as much about status effects as it is about Poison-types. Plus the Ghastly line does know Hypnosis...

Team Rocket's plan was to recapture Mewtwo.
  • Think about it. They stole the Sliph Scope, which let them see and capture Ghost-type Pokemon, which Psychic types are (supposed to be) weak to. And they also steal the Master Ball, which provides a 100% capture rate. Giovanni had already convinced Mewtwo to work for him before, but never actually captured him, which lead to Mewtwo betraying him. So this time he is intent on capturing him in order to force him to work for him. He may even put the armor back on him, just so he can properly rule Kanto, and possibly even Johto, Unova...the WORLD!

When all of your Pokémon faint, the trainer or wild Pokémon you were fighting then attacks you, the trainer, knocking you out.
  • When you run out of usable Pokémon, the game states that you "blacked out". It's never made clear why this happens; there's nothing really stopping you from imagining that whoever you were fighting then set their sights on you and beat you shitless. It very much makes sense in the case of wild Pokémon; maybe less for trainers since it implies that all trainers are violent bastards, but it makes even less sense to me that the player character would be so traumatized by one defeat that they fall into a dangerous panic attack.
    • It's conceivable that it was meant to be 'backed out' - ie the player retreated from battle - but was Lost in Translation. The fact they later changed it to 'whited out' did not help matters.
      • This seems to be supported by the text pieces in FR/LG, talking about the trainer sheltering his/her fainted Pokemon and rushing them back to the Pokemon Center. Doesn't make sense if the trainer passed out. (I've always wondered why they didn't keep those bits in later games, they were nice.)
    WMG/PokémonPokémon Gold and Silver
PokémonWMG/Video GamesPokémon Black and White

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