Pokémon Mystery Dungeon/WMG

The Rescue/Exploration Team Badges provide a psychic link between teammates
The badges are made using super advanced junk Pokémon found that humans left behind. The badges provide a temporary psychic link that allows the rescue or exploration team to see what each other sees and share the same bag (which, by the way, is a small dimensional hole). The badge can also be used to teleport Pokémon out of dungeons, but only if they are not the leader. For that, an 'Escape Orb' is needed to provide more power. The badges can also teleport a team to certain relays across the continent, which is how you can get to places so fast. The regular series's gym badges are probably prototypes for this tech.

In the generation V PMD games, there will be a Swoobat functioning as the Chick Magnet.
Firstly, Swoobat is favored in the human world by cheerleaders and other such people. Plus, it uses hearts as it's motif, so why not? And on top of all this, we have Rule of Cool and Rule of Cute.
 * Oh yeah and it learns attract by level up.

The Judge of Darkness in Murky Cave from Red/Blue was really Giratina or Arceus
How else would it be able to allow someone to enter another persons heart?
 * Since when could Arceus OR Giratina do that? And even if they could, those two didn't even exist back when the game was made.
 * That hasn't stopped anyone before.
 * I'm talking in-universe not out.
 * Anyway, given the appearance of Munchlax in debug mode, it would be possible that GF had already thought up one of the two by 2005.

The dungeon-dwelling Kecleon take over Monster Houses for their shops.
While finding items in mystery dungeons is pretty easy, the best stuff tends to be inside Monster Houses. The Kecleon are aware of this, so they specifically seek out Monster Houses. When they find one, they summon their buddies, slaughter everyone inside, then gather up the goods and set up shop. That's why Kecleon are so strong and how they're able to instantly call in help if any adventurers try to swipe their stuff.

The Wigglytuff who sold Friend Areas in the first game is the Guildmaster in the second.
Explains why Friend Areas are no longer necessary and how the two Wigglytuff act similarly.
 * Alternately, he could be that Wigglytuff's son; we do get to see his parents and some of his past in his sidestory, after all.
 * This could be Jossed, as the second game establishes that it takes place in the past. Unless the first game also took place in the past, before the second one...
 * Pretty sure the Wigglytuff in Red/Blue is female. I remember the partner Pokemon referring to Wigglytuff as a "she."

The Dugtrio in Time/Darkness/Sky is the Diglett from Red/Blue Rescue Team.
There was actually a Time Skip between the two games; during that period he grew up and set off on a journey to find himself. His father was a braggart who exaggerated his own experiences to sound better; whether he was aware of this or not, he wanted to live up to that 'legacy' and have adventures of his own. Thus, he traveled across the sea, then joined Wigglytuff's Guild. He also had a son of his own and is raising him to become an explorer as well.

Everything in Time/Darkness/Sky is Bidoof's Fault
Bidoof wished to Jirachi that he could have friends. That caused Darkrai to rise to power and spin his evil schemes to dethrone Dialga and Palkia, which caused the complex series of events leading to a human getting trapped in the body of a Pokemon and joining the guild, thereby granting his wish. Never, ever mess with probability!
 * Assuming that Team Charm's special episode takes place a fair ways into the past (say, a decade or so; they're not yet famous, and Wigglytuff's still exploring solo), then no, Bidoof's wish can't be it, because Darkrai had already taken the Time Gears from the Temporal Tower by that point (quite the slow-acting plan, by all implications), and Bidoof's spent maybe a few months at the guild (at most) before the story starts.
 * You're forgetting that time travel is involved in this game.
 * No, I'm not, but where are you going with this? The Time Gears were already established as not to be removed from the areas Darkrai hid them in by that episode, I don't think rumors like that spread through time travel, just good ol' word-of-mouth.
 * For one thing, it is never explicitly stated that Darkrai stole the time gears from Temporal Tower. If removing the time gears from Temporal Tower was directly responsible for bringing down the tower, then Dialga must have been okay with them being gone during his gradual descent into insanity. (It is speculated by many that the gears are okay being hidden around the world, that placing them back into the tower is simply a fail-safe mechanism in case Dialga loses control for whatever reason, which was needed after Darkrai sabotaged the tower.) For another thing, Darkrai travels through time. Upon awaking he could have warped into the past to begin his scheme long ago, creating a Stable Time Loop.
 * There is nothing hinting that the "return the time gears to the Tower" thing is a mere failsafe; certainly the way Grovyle kept talking about it implies that the Tower is the gears' original location.
 * Considering the Time gears are implied to regulate the flow of time in the specific region they're in, it doesn't seem likely that Darkrai stole them to destabilize the tower. This is only helped along by the fact that removing one stops time in that area, which, if the "Stolen by Darkrai" theory were true, should not occur.
 * I think the time gears regulate time (as time did go out of control in the area around where it was kept once it was removed) but the failsafe at Temporal Tower resets that. Or, perhaps Darkrai might try to destroy a time gear and they were hidden so the failsafe could be turned on.

Alternately, Bidoof's Wish helped save the world.
Remember how Jirachi warned him that "it might take a while?" That's because the threads of fate first had to be cast out before he could work with them. In the original timeline, nobody came back to the past to fix things -- therefore, your cowardly partner lost their Relic Fragment on the beach that day and never worked up the courage to join the Guild. When your hero and Grovyle made their trip back and the hero got thrown off course, Jirachi secretly stepped in, working his magic to help turn them into a Pokemon (rather than just plain die) and ensured they landed safely on the beach -- putting them right in their future partner's path and ensuring they'd be able to help recover the Relic Fragment. That way, your amnesiac hero would gain the experience and strength needed to ultimately fight powerful Pokemon and save everything, and Bidoof got his buddies. Everybody wins!

Giving out Eggs as rewards is just how adoption works in the PMD world -- or at least in Treasure Town.
There aren't any orphanages or other such services available, unless you count Chansey's Daycare... and even then, she only cares for the eggs until they hatch. If you want to ensure that a hatchling you can't care for yourself is going to be well taken care of, your best bet is to seek out an exploration team or other responsible-looking individuals and hope they accept it.

Magnezone's police are severely understaffed.
With the outbreak of bad pokemon everywhere, most of the police's resources are being sunk into mantaining the prison system and ensuring offenders don't stage a riot or break out. As a result, Magnezone can't send out many officers to catch crooks -- he's barely able to mantain a backup escort for himself! Thus, he worked out an agreement with Wigglytuff's Guild to post bounties. There's no shortage of exploration teams passing through, of all different types; they help ease the crushing workload by taking down criminals (especially ones Magnezone wouldn't be well-matched against), and let the police take care of the cleanup.

At least some of the recruits who join your team are circumventing the whole Guild system.
Joining the Guild means signing away most of your profits and having to put up with Chatot all the time... is it any wonder Pokemon might be put off by more than Wigglytuff's reputation? By contrast, joining an apprentice's team may mean being barred from "offical Guild expeditions" and the like, but you still get to go on most adventures, getting stronger and more experienced... Thus, certain Pokemon (particularly the ones who join in Treasure Town) may simply be exploiting a loophole, and intend to branch off into their own Teams at some point in the future.
 * Well, going off the being barred from official guild expeditions point... I'm pretty sure Chatot actually referred to your recruits as not being guild members. So I'd say that this guess is actually pretty close to canon.

Wigglytuff's Guild helps fund the various businesses in Treasure Town.
Only a few of the shops charge enough to earn an independent profit; the others are supported by Wigglytuff's goodwill. That's why the Guild takes so much of the reward money; they aren't just covering their own expenses, they're ensuring that Kangaskhan, Spinda, Marowak and the others can stay open.
 * The Marowak Dojo's backstory folds nicely into this: the original owner had to close up shop because he couldn't afford it any longer. After the Wigglytuff Guild was formed and he started supporting the other shops, Marowak was able to ask for financial support and reestablish it.

Team Skull died from the injuries they sustained during the late game.
In Time/Darkness, their last appearance is in, heavily wounded. Having them die there casts their seemingly lighthearted chat about how they helped fix a problem they caused in the first place in a very different light. They don't honestly think that one act makes up for a lifetime spent hurting others; it's just easier than reflecting on how their selfishness and greed led them to a violent end. They know they're dying; this is just their way of going out with a smile.

Humans are extinct by the time of both Mystery Dungeons.
Why don't any humans ever show up in the Mystery Dungeon subseries besides the PC? It's because they went extinct long ago, and are remembered only for assorted ancient artifacts.

The heroes were pulled from the past.
Perhaps Dialga or Celebi did it.

The Time/Darkness/Sky hero was revived.
Grovyle somehow had one created from preserved DNA so he could partner with him/her and use the Dimensional Scream ability.
 * Perhaps Mewtwo helped.
 * Alternately, Ho-oh did it, gifting some random - or maybe not-so-random - set of bones life and additional abilities (ie the Dimensional Scream), like how he revived the Legendary Beasts.

The two Mystery Dungeons are in the same world. The PMD2 hero is a foundling.

 * This troper has a theory. I'm assuming that PMD1 and PMD2 are in the same world, but generations apart. Whether they also share a world with the mainstream games is up to you. Anyway, my theory is as such: some time before PMD1 took place the world was inhabited by both humans and Pokemon, but humans eventually left the world for some reason leaving Pokemon behind. It can't be long before PMD1 because several human constructions are still standing. Eventually, generations later, at some point between the present of PMD2 and the future of PMD2 the humans return, and are all but wiped out by Primal Dialga, leaving only a few humans left, including the player, probably as a baby. One by one the remaining humans are picked off, leaving only the player, who is taken in by Grovyle. The rest is history. Future history.
 * I think you've got it. If what you said is true then that means that the 'world of humans' mentioned in PMD 1 is the past, and that is where you were pulled from. That really explains everything, good job!
 * My theory is that the humans left the PMD world before the first games for some reason, and some humans returned (along with the player as a baby and his parents) after everything went to hell in the Bad Future of the second games. Then Primal Dialga picked off those humans, but not the player's parents managed to hide him until Grovyle found him.

Humans are alive and well, but the Pokemon towns are far away from them.
Apparently humans very rarely visit, if ever.
 * I always thought this was true as well. It explains why all the Pokémon know what a human is, even though you don't actually see any in game.

Actually, both Mystery Dungeons take place in the very distant past.
Explained in the Explorers games. However, in the Red and Blue games, time isn't being messed up. Anyway, the games take place in the past before humans even appeared. This would suggest that Pokemon are the original inhabitants of the world. Humans are either aliens or descendants of the Pokemon. Finally, the world that PMD2 takes place in is the same world where the original is set. The original area is simply the mainland, maybe even part of a larger continent, and the PMD2 world is simply an island off the coast of the main landmass.


 * Except in PMD1 one of the Friends Areas is described as being a 'ruined human laboratory', so it can't have been in the distant past.


 * Best part is that you can use legends to help support this. One of the old legends implies that Humans are skinless Pokemon, and that they took off the skins before going into villages. This could be a bit before Pokemon started doing this, and why there are a few, although rare, humans, and why some Pokemon freak out a bit when they find out that you are human. After all, you are essentially a Pokemon who


 * If they took place in the distant past, then where did Mewtwo come from? What about the Porygon, Voltorb, and Magnemite evolution families?

In Time/Darkness/Sky, Dimensional Scream is an actual Ability
An "Ability" is, of course, different from an ability. Much like how some Pok Ã©mon have Abilities like Static or Poison Point, some humans have the Ability Dimensional Scream. It is unique to the species, and perhaps fairly rare. This only leaves the question of what the other human Ability is.
 * It's probably something along the lines of "Nonfluent: This Pokemon can't understand a word anyone else is saying."
 * Which would suggest that the PC could converse with Grovyle even before being transformed.
 * Well, there was that flashback/dimensional scream at the Groudon statue.

The Mystery Dungeon Pokemon are descendants of uplifted 'mons.
The mainline Pokedex suggests that at least some and probably most Pokemon aren't sapient. In the Pokemon Mystery Dungeon games, every Pokemon you meet is definitely sapient. The solution? Many generations before the Mystery Dungeons, when humans still walked with Pokemon, they used some process to uplift every single non-sapient Pokemon species. In fact, this was the entire reason humans came to the Pokemon planet. Yeah, they're aliens.

The process of uplifting so many species took humans many generations, enough that their little band of colonists at the beginning eventually expanded to cover the whole planet. Most sapient Pokemon we see in the mainline games are members of already-uplifted species; it's possible that Trainers are an integral part of this uplifting process. Anyway, once every Pokemon species had been suitably uplifted, humans withdrew from the planet for their next project.

An unfortunate flaw in the process means that uplifted Pokemon and their descendants will potentially revert to a crazed, non-sapient state during periods of extreme stress, and that's just what's happened to the wild Pokemon wandering around in the Mystery Dungeons. Calming them down by punching/biting/clawing them until they faint naturally makes a few come back to their senses when they awaken.


 * What about Wobbuffet? He acts just like Wobbuffet in the anime.
 * Null and void, in the orginal, Wobbuffet is always saying "????? s? na-n-su" (which roughly means "that's the way it is" in Japanese). Same goes for Wynaut - he's always saying " ???? sohnano" (which means 'really'). These two words sound simular, and make a pun: "Really? That's the way it is? Really? That's the way it is? etc.". Also, both these phrases make a handy rebuttal to anything your character says.

Some of the international translations had a go with this - but the English didn't. Also, this is why Jessie's Wobbuffet is always popping out of his ball. He's saying: 'That's the way it is!' (like when they blast off or think of a plan!).


 * So basically, Wynaut and Wobbuffet are saying "O RLY" and "YA RLY"?

Love the theory, by the way! But what about the hero(ine) in PMD2's human power? The Dimensional Scream could be a power the humans obtained in the future. This power could be used as a back-up to the human's technology. But the human must be with some one they trust for it to work (preventing the power being used under torture!). Using this power, the human (if trained it enough) would be able to find the fellow humans, allowing them to follow them to the next planet after making the Pokémon world sapient.

This also another handy ability. They could check the past and future of their experiment, so they would seldom/never need to return to the experiment. (Please add to this if there's a flaw, it's been a while since this troper played the PMD games).

Dusknoir's ancestor used a Master Ball on Primal Dialga.
When everything started going pear-shaped in Mystery Dungeon 2, various Pokemon attempted to get control over Primal Dialga in a vain attempt to restore his sanity. At some point, a Dusknoir (or a lower Pokemon in the evolution chain) found a curious relic left over from human times; it proved to be a Master Ball, and this ancestral Dusknoir used it on the raging time god. It obviously didn't fix much, but this is why the Dusknoir of Grovyle's time seems to act as both Primal Dialga's enforcer and keeper.
 * Alternatively, Dusknoir is descended from one of Dawn/Lucas' Pokemon.

The Mystery Dungeon Pokemon are descended from genetically altered Pokemon.
The land of Mystery Dungeon did have humans, but they all died out. Before that time, a group of scientists genetically altered their Pokemon to be much more intelligent, cooperate with each other, live in houses, and use money. Poke is the currency the humans used.

After the other humans found out about the genetically enhanced Pokemon, the scientists and Pokemon were driven from the land. They landed in Mystery Dungeon Land and colonized. The humans built the Friend Areas Power Plant and Decrepit Lab for themselves. They also built the beginnings of Pokemon Square.

Eventually, the humans died out. The Pokemon bred with the native Pokemon and created intelligent, competent Pokemon - the Mystery Dungeon Pokemon. The Max Elixirs, Proteins and TM's were created by the scientists and left behind. The Pokemon now live so well because they are so intelligent. Nowadays, nearly every Pokemon is related to the genetically altered Pokemon. Also, the gummis were a kind of fruit altered to enhance intelligence.

Primal Dialga is not responsible for any of his actions.
He's gone every bit as wild as the Pokemon you meet in the Mystery Dungeons by the time Temporal Tower collapses. He's relying more or less completely on instinct, and is only just rational enough to express his feelings and vague concepts via telepathy, primarily to Dusknoir, his "Trainer". Any appearances of a higher degree of rationality or planning is the result of Darkrai acting like a voice in his head.
 * Why is this thing in the WMG page in the first place?! It's already established that Primal Dialga was under control from someone else, though I remember the culprit to be Darkrai, and Dusknoir the mercenary that Darkrai hired indirectly through Primal Dialga.
 * I'm pretty sure the "relying completely on instinct" bit was also established in the game.

The Arbok of Team AWD and the Medicham of Team Charm were once members of Team Meanies.
Call it youthful indiscretion? It wouldn't be the first time a couple of kids fell in line with some jerk promising grand things -- "Oh, we'll rule the world one day, you'll see!" Eventually, of course, the team drifted apart, and after Gengar had to take care of plot-related details, Ekans and Medicham went their seperate ways. Both ended up as part of new groups, Ekans evolved, and everything worked out pretty well. (Plus, this theory makes certain events in Sky more... interesting.)
 * Does that mean that Team Charm's Gardevoir is the same one rescued in the first game?
 * It's possible, but in when Team Charm and Team AWD face off in Special Episode 4 in Sky, wouldn't Medicham and Arbok have recognized each other? Or at least, Arbok would've recognized Medicham?

The Dimensional Scream functioned differently in the future due to just how horrible the world had become.
Normally, the Dimensional Scream gives its bearer important information that can be used to avoid danger or keep situations from getting worse. For instance, had the hero heeded their first visions, they could have completely defused the situation before it unfolded; similarly, the visions at Waterfall Cave let them find their way through quickly (instead of dragging out a potentially dangerous search of the area) and could have helped avoid a major trap.

However, in the Bad Future, everything is dangerous -- there's no relatively "easy" way to avoid peril. Dangerous Pokemon are running wild, time itself has gone insane, the only order imposed on this world comes from evil minions... and all this was sparked off by Temporal Tower's degradation. Therefore, the "simplest" solution is far from simple: fixing the problem in the past. And for that, they need the Time Gears. Thus, every vision in the future is linked to the Time Gears, as that's what is needed to save the world. The Dimensional Scream doesn't offer information on any other options because it can't see any.

The Dimensional Scream can be controlled; however, the Hero never received any such training.
After all, in the future, the only visions they recieved were linked to Time Gears. They weren't aware that this wasn't the only function the Dimensional Scream had; thus, even if they'd retained all their memories, recieving other visions in the past still would have shocked them. With proper training, they could control when they have such visions, and possibly even aim for specific information; however, without a knowledgable source to recieve such training from...

Grovyle is Yami Yugi
After Yami  he became entangled in another dimension and was transformed into a strange creature. This explains why Grovyle's disposition and attitude is similar to Yami's. Seriously, just listen to his voice in the TV special.
 * In addition, based on his near-loving obssession with the sea, Dugtrio is Mako Tsunami. Probably the abridged version. He even claims the sea can talk at one point (saying it wishes the hero and partner good luck).
 * Maybe it's because he's voiced by DAN GREEN!!!

The main character from the second TV special is actually a girl
Seriously, that's a dude? He (she?) sure sounds a lot like Beauty. I'm pretty sure the two are related...
 * Well he never said that he was male so...
 * No, it's a he. I'm pretty sure he's referred to as a 'young boy' right at the beginning of the episode.

Time is tied to both Dialga's mental health and his physical health.
Even with the planet paralyzed in the bad future, Pokemon can still move around, and enough presumably grows to keep at least some people fed. Time hasn't completely stopped, just in a lot of important ways. The reason why is that Dialga is crazy, but he's still alive; if he should die, time would stop completely and the world would truly end.

No Time Travel was involved at all with the Explorers games.
Maybe the games aren't set in the past. Maybe the games are actually set in an Alternate Universe. The player character did not  because of a change in the timeline. ''This was actually part of  After Dialga came back to his senses, he reversed this process and brought the player back.
 * Magnezone has assumed this was canon from the get-go. Imagine her confusion finding such a thing on WMG alongside wonders like Grovyle = Yami Yugi...
 * Ironically, I was the one who wrote that Yami Yugi one...but I was just being funny. Anyway, to expand on and correct this theory, the player's disappearance could have actually been the result of a timeline change. However, the player character didn't cause this. Darkrai had been manipulating Primal Dialga into erasing the PC and Grovyle from the timeline.

It is taboo to mention someone's real name in public.
The Pokemon do have names besides their species names, but for some reason there's a strong taboo against using them in public. Not even the confusion of having, say, two Kecleon running a shop or is enough to overcome it. The Pokemon that join your team signal their working relationship with and trust in you by telling you their real names, and Alakazam, Chatot, and so on probably refer to the hero and partner by their species names. The partner is forward enough to ask the hero's name at the beginning as they can tell the hero's extremely dazed and probably needs all the bits of memory they can get.
 * Perhaps using a given name is an extremely informal method of address, used primarily for close friends and those of lower status.
 * Would you believe me if I told you I have an (unfinished) fanfic using this very idea, that I wrote before reading this WMG? Because that was pretty much the best idea I could work up that allowed me to name the protagonists, as having protagonists named with the generic names of their species could potentially cause apathy in the audience as to their story.

All Pokemon have unique names; the games simply omit them because of Nominal Importance.
The only Pokemon whose names matter are the ones the player inputs themselves: The Hero, his/her Partner, and everyone they recruit. Everyone else has names; the game simply doesn't use them because this story is ultimately all about the hero and their friends. Wigglytuff's name isn't mentioned because the Guild's called "The Wigglytuff Guild", and revealing his real name would just confuse the target audience, wouldn't it? Same goes for Chatot, Bidoof, Sunflora and the rest: it's easier to just address them by what they are and conserve details rather than juggle extra names. Plus, this lets any fans who really care about such details to invent their own, putting that much more of a personal spin on their version of the story.

Pokemon belive in the Power of Names, and thus only reveal their "real" name to close allies (unless they are a transformed human ignorant of this view)
As seen on the Black and White WMG page.

The Time Gears were originally hidden around the world long ago to avert another crisis.
At some point in the distant past, time began warping itself in certain areas. This may have actually been  first attempt at paralyzing the planet; they found a way to make time chaotic in small regions, moving them out of sync with other lands. Pokemon around the world began going wild, mystery dungeons started appearing, growing more numerous and unpredictable as time slid further and further out of control.

In order to prevent time from completely collapsing, Dialga permitted the Time Gears being removed from Temporal Tower and strategically hidden in the regions hit the worst by time's decay. This stabilized time as a stop-gap measure, but it would take centuries for the lands to heal. Thus, Dialga left them where they were, figuring this arrangement would be fine for a few centuries or so -- Temporal Tower wasn't in any danger, standing strong and proud. So long as all Pokemon knew that disaster would befall them if anything happened to the Time Gears, it'd work out just fine, right?

Of course, this also gave the scheming villain plenty of time to work with these arrangements... Over the centuries, they gradually undermined Dialga's plan, ever-so-slowly chipping away at the stablility of time and Temporal Tower. These changes were so subtle and minute that they were effectively Gaslighting Dialga; that, combined with the slow-but-steady deline of Temporal Tower, eventually left Dialga in a state of ever-growing madness. Thus, he was in no position to counter the enemy or stop the next phases of their plan... naturally leading to the events of Explorers.

The voice of the Luminous Spring is a Mew.
Mew are the ancestors of all Pokemon, so it'd make sense that they'd be in charge of helping everyone evolve. Also, it would be awesome.
 * Mew are supposedly the ancestors of all Pokemon. Arceus makes more sense anyway, or perhaps there's a legendary in charge of evolution we aren't aware of yet.
 * In the debug menu, Jirachi is the pokemon that acts as the voice for Luminous Spring. What does that say?
 * What? Mew is the Ancestor, Arceus is the Creator God, what's the confusion? Ancestor means, '[Being] from which [Blank] is descended from', The only beings descended from Arceus are the Dragon Trio and the Lake Trio... Unless Gamefreak makes some other stuff. Mew is just the first Mortal Pokemon, like Adam and Lilith/Eve are to Humans, it's not a god or anything.

Palkia is responsible for creating Mystery Dungeons.
None of the Pokemon seem to know or even care why the same dungeon is different every single time you go inside. The existence of Dialga and Palkia has also been shown to be a little less than common knowledge. It's reasonable that Palkia could use its powers over the fabric of space to keep these dungeons constantly rearranging themselves. The Pokemon inside these dungeons could even be attacking you as a side effect of being exposed to these powers. When you beat the crap out of one, sometimes you knock enough sense into it to make it want to join you.

The Explorers Partner is an orphan.
They're called a 'kid' more than once over the course of the story, and yet lived all alone just outside of town until joining the Wigglytuff Guild. Childcare seems to be hard to come by for orphans if Chansey's Daycare is any indication. Joining the Guild was as much about getting some kind of family as it was about shoring up on confidence and experience.
 * I just assumed that the "kid" epithet was more due to their rookie status.
 * If you look at it another way... perhaps Bidoof's wish caused the partner to suddenly exist when it hadn't before. Since the partner has no family, of course they're an orphan!

Berries are the Pokemon-world equivalent of energy drinks.
Ever wondered why they cause immediate rejuvenation? This is made even more evident in the first TV special, where they cause whoever eats them to suddenly perk up or become hyperactive.

Gardevoir from Team Charm is the same Gardevoir from Red/Blue Rescue Team.
Sometime after being released from Ninetales' seal in Murky Cave, and with no memory of why she was sealed in the first place, she decided to strike out on her own. Eventually, she meets Lopunny, who invites her to join her Rescue Exploration Team, and she accepts. They later meet Medicham, and the rest is history. This theory helped by the fact that, statistically, Gardevoir seems to be the most experienced of the trio. (highest level, etc)
 * Gardevoir appeared in town and joined the player's team after being freed in the original dungeon games.

Spinda is as high as a kite.
Do I really have to explain this one?

Ludicolo is the Kool-Aid Man.
Oh, yeaaaaah!
 * That makes so much sense. They even look alike!
 * Or he's Macho Man Randy Savage in Pokémon form.
 * Um... about that...

The Duskull running the bank is the present-day version of Dusknoir.
Since there only seems to be one significant member of each Pokemon species, it's unlikely that there's another Duskull running around during the events of the game.
 * So... why doesn't Dusknoir have Duskull's Verbal Tic?
 * This is because he decides to drop it between the time of the main plot of time/darkness/sky and the dark future that's ruled by Dialga.

The reason the Time Gears weren't at Temporal Tower was because they'd never been there.
OK, so on the Just Bugs Me page, someone asked why the Time Gears weren't at Temporal Tower to begin with. My theory: they were never there. The Time Gears were at the same place as Temporal Tower, guarded by Dialga, until someone raised the idea of building a real tower. Dialga was one of the most important Pokemon involved in building the tower, but this left the Time Gears unguarded for anyone to play with, so he asked Mesprit, Uxie, Azelf, an unknown guardian and Ditto's predecessor to take them to somewhere far out of the way until the Tower was finished. However, just before the Tower was finished, there was an earthquake which damaged the Tower slightly but also killed the guardian in Treeshroud Forest. Dialga had been hit on the head by debris in the earthquake and forgot that he needed the Time Gears there- he thought that time would work fine the way it was, and by the time the Pokemon had recovered from the effects of the quake, the guardians didn't give the Gears back because Dialga hadn't asked for them and it had been a while since they'd been given them, so they just kept them. Over the years, a legend started about how the Gears needed to be at their present locations, and soon Dialga started believing it- especially when someone moved the Treeshroud Forest Gear to see what would happen and time stopped.

The player character in Time/Darkness/Sky was created by Giratina.
In the Dark future, Giratina kept his world separated from the paralyzed world, but seeing as the few remaining Pokemon that were still trying to fight Primal Dialga, Giratina decided to help them before sealing his world away from their's permanenlty. He called upon Grovyle and Celebi, and told them how they could change the past in order to save the future. He then created the player character specifically to help Grovyle and Celebi with this mission, and used it's power to make sure that the child would age to the proper age for effectivily being able to help out with such a dangerous mission.

Chatot is Younger Than He Looks.
He's actually just about as inexperienced as the rest of the Guild. Sure, he's Wigglytuff's right-hand bird and has shouldered the responsibility of keeping the Guild running, but that doesn't necessarily mean he's an adult -- at most, he could be a teenager. He hasn't finished growing up yet, and lacks the maturity that age and experience should bring. Factor in Wigglytuff's own childish nature, and you have somebody who believes they're the Only Sane Man, which has grossly inflated his ego.

That's why he makes such stupid, snap decisions all the time -- for all the responsiblity he holds, he's still Just a Kid.

The Adventure Squad trio of games are Lighter and Softer as part of a Batman Gambit by the developers.
The Explorers games got a LOT past the radar, so just in case the Moral Guardians happened to catch wind of that, the Adventure Squad games are Lighter and Softer by comparison. This way, the Moral Guardians won't find anything objectional and will dismiss the series as "kiddie fluff"... at which point the fourth games will spring the Surprise Creepy on any players lured into a false sense of comfort by the third trio.

The Mystery Dungeon Series takes place in Pokemon Storage Network
The whole shebang takes place in the Pokemon Storage network inside of the main games, sometime after the original games, as early as Gold/Silver. I know only the following in support of this theory.

Bill from the main series is introduced as having turned himself into a pokemon of some kind during a teleportation device accident. The Pokéballs (And PC boxes) are described to be able to make an environment the captured 'mon likes. The PC network from Bills storage system has a central server, where all the Mon's are stored (Elsewise, you could never reach them from just anywhere with a PC.)

Bill, after his teleporter incident was confused as to whether he was human or not.

So my wild mass guess:

The Player Character is sent intentionally into the PC network to check the program for errors. This explains why the levels are randomized: The infinite challenge and stimulation keeps your Mons in storage from getting bored. The Time Gears are physical manifestations of the Kernel that underpins the whole system, and the places like Treasure Town or whatnot are mass hubs on the Central Servers where the Mons are left free.

Time is also accelerated from the outsider's perspective. That's why humans and their appearance are common knowledge, but their absence is unremarked upon, as they know deep down they're in some kind of deeply involved simulation.
 * Out of curiosity, what does this mean for the I Choose to Stay part of the Rescue Team games, or the ending of the Explorers set?
 * As soon as I get to the ending, I will provide an answer. As for Red/Blue, the Hero lost their memory- this may have even been intentional, (sabotage or other reasons), at least so as to minimize the odds of getting lynched by irate mons. (Or worse yet, given a list of bugfixes.) If it wasn't intentional, then the transfer was screwed up somehow. Either way, as noted above, they can't remember much if anything of the world they were from, so they simply figure 'what the hell' and stay.

I will get to the ending of Sky and answer you. Chapter 10 so far...

The game takes place in an Alternate Universe...
...where Lance succeeds in destroying the world in Pokémon Special! Lance said that after his plan succeeds the world would be entirely populated with Pokemon except for a few skilled trainers after he succeeded in his plan, so the humans that are left after the apocalypse would have likely died out. A few decades after humans become extinct, the Pokemon would start to develop sentience (if Pokemon "evolve" all the time, they'd likely develop that in a situation where there are no humans around), and the rest is probably history. Pokemon probably know about humans because there are still remaining ruins of human civilization (it's probably no less than fifty, and no more than a hundred years past the destruction), or because there were legends that told about humans.

However, this can't solve the problem as to where the human protagonist in Time/Darkness came from in the future, which leads to my next WMG...
 * Maybe the player character is descended from the trainers Lance selected? While there would only be a few of them, yes, that would actually help explain why the protagonist is a human but we see no other ones. There were so few humans to start with, that they left very, very few descendents behind. They probably had some form of specific population control to ensure that there were still a few people around, but not too many to keep them from abusing the Pokémon.

In the future, time is horribly distorted.
Because of that, the past would in some way start to overlap with the present at certain times, which probably made the human protagonist come to the future. The rest is history.

Grovyle from Time/Darkness is the human protagonist from Red/Blue.
I mean, this is a WMG page after all.

The Pokemon that serve you were on your side all along. (Red/Blue)
Before you head off as fugitives, you are able to buy things, store things and link moves ect. It seems a bit odd that the stall Pokemon are able to serve you, specially while asleep. They only pretend to be asleep to avoid detection and therefore be seen as a follower of the main character, as that would make them "the enemy".

Luxray and Manectric's tribes were both involved in the betrayal at Amp Plains.
The two tribes used to coexist peacefully there, but at some point, a deadly misunderstanding occurred, leading to an abrupt, vicious turf war breaking out. At the time of the game events, the two packs maintain an uneasy peace, venturing to the Far Amp Plains at different times... and always on edge, half-expecting the other side to betray them again and launch an ambush.
 * And in Explorers of Sky, your partner can be a Shinx... no wonder the Manectric tribe doesn't believe you!

The reason why the Dimensional Scream works differently in the past and the future
Time and Space are "constant" forces in the world which encompass and surround everything, somewhat like energy fields. The Dimensional Scream now reaches from inside the person out into these energy fields (Time and Space) and accesses them. This is how the visions are generally caused.

Now, in the future, time has stopped, so one of these 'fields' is as good as nonexistent. However, the locations of the Time Gears are essential for the continued flow of time, right? So maybe these locations were some sort of 'focus points', where time ran especially strongly in the past; in the future, however, they might be the only place where residues of 'Time' can be found (as I said, I'm talking about time as some sort of field or energy). That is why, in the future, only places related to the Time Gears caused the Dimensional Scream.

In the past, however, time still flows everywhere. As such, the Dimensional Scream can be triggered not only near Time Gears, but also in totally unrelated locations.

The Treasure in Mt. Bristle Drowzee thought was money and etc. was actually a time gear
That's usually what most of the treasures turn out to be, unfortunately.
 * I'm sure the game states at some point that there are only five Time Gears. One in Treeshroud Forest, one at each lake, and one at that place that appears in one of the sky extra missions. See the entry below.
 * Actually, there was another one that was shown to be inside a volcano, but it was never seen in the game, only in a cutscene. If Mt. Bristle is a volcano that hasn't erupted for years, it could explain where that Time Gear was.
 * Also, I thought it was never stated that there were only five, just that there were at least five. I think Grovyle even said he had all the "necessary" ones, not specifically all of them. So it is possible that there could be a Time Gear hidden in Mt. Bristle.

The player character is asleep in a hospital on life support. The reason he/she stayed is because he/she doesn't want to wake up.

 * Why all these horrible WMGs? Why does everybody want to think of the worst?!

The reason Grovyle goes back to the future is not because he didn't have enough strength to continue, but because of Celebi.
What other reason could he have? He's still got enough strength to push Dusknoir around, so he could've continued, but didn't because he wanted to spend his last moments with Celebi.

There exists more than five time gears.
Well, at one point we do hear that a time gear was said to be hidden inside a volcano, but none of the five time gears we see were inside one. There may exist other time gears, but only five were needed. After Temporal Tower was restored, it's possible that Dialga drew away the power of the remaining time gears hidden out there to make sure that he would be powerful enough to prevent time from ever going out of control again.

You're an orphan with no friends.
That's why you don't care about your family in any game, and in the originals you didn't care about former friends or any connections. You're more than content with staying.
 * World of talking animals and awesome adventures > School, homework, work, your boss/teacher, over-restrictive parents, annoying little brother, etc any day!
 * But the player has no memory of his family or friends in the real world. Would you rather go to a world where it's a crapshoot whether or not you were accepted in life, or stay in a world where you already have friends, one of whom would be particularly distraught at you leaving?

The first Wigglytuff is the Guild Master's mother
As in the one from the first game.

These Pokemon are more evolved then their main game counterparts
Our meaning of evolved, not the metamorphosis kind in the series. They're sapient for one thing. They don't appear to follow any animal instincts like the main game Pokemon. They don't hunt and they all appear to be either herbivores or omnivores. They naturally get along with other Pokemon no matter the species or gender. They have a better sense of the world then most Pokemon in the game continuity and they can create buildings. Due to the lack of exposure to humans and human things however, they still don't understand certain things, such as potions or computers.

The Pokemon aren't talking.
It's Translation Convention. In PMD2 though, you may or may not have been able to understand Grovyle when you were a human.

You and many important characters in the Rescue Team games are sharing dreams.
The partner and the citizens of that world are projections. This explains why you woke up in an entirely different place and have no memory of how you got there.

Dialga brought back the PC in Time/Darkness/Sky to prevent a Temporal Paradox.
If the future you're from no longer existed, then you never existed and therefore could never have saved Dialga in the first place.

The mons are M.D.C creatures
It explains how they can survive things that can kill a normal human being.

The (human) player was resurrected from a fossil.
Probably the Pokemon managed to find a way to bring human fossils back to life.

The Mystery Dungeon world is an alternate universe where N's plans succeeded.
N wants to create separate worlds for humans and Pokémon, right? This would explain why the Pokémon in Mystery Dungeon know of humans, but none appear.

Dialga isn't the god of time, he's the personification of time.
Temporal Tower was his original home, and his powers became tied up with it. The Time Gears were just ordinary pieces of the tower. Dialga's power soaked into the stones that made up the tower and gave individual pieces the ability to maintain time. When time began to screw up in certain places, Dialga removed the stones and allowed them to be taken to the afflicted places, but since Temporal Tower was no longer whole, his sanity began to deteriorate.

Perfect Apples are drugs
Seriously, you can replace the word "Perfect Apple" with the name of any illegal substance and the whole ordeal would still make sence. Also note how cranky Wigglytuff gets.

Temporal Tower is the PMD Universe's manifestation of The Dark Tower, and both stories are interrelated.
Both towers hold time together, and the protagonist in both stories are trying to stop the towers from becoming destabilized. Your party in PMD is your Ka-tet, and instead of a gunslinger you're a member of the guild. Dusknoir is a incarnation of Randall Flagg/A Servant of the Crimson King.

The Grandmaster Of All Things Bad is Satan
He takes on the appearance of a charismatic individual in an effort to gain everyone's trust while hiding his true power. He speaks openly of peace and the goodness of all living creatures, while having no problem using violence to solve all of his problems and increasing his numbers to overrun the opposition. Most obviously, he offers the main characters great power and tempts them with an apple, leading to their immediate fall, and admits his true identity afterward.

A future PMD will connect the mystery dungeons in that title to the Dream World.
This will be used to explain their random nature, as well as give the developers an excuse to use the alternate Dream World Abilities and moves for all the pokemon. (This will be handled the way they already handle pokemon that have multiple potential Abilities: they'll just have both.) At first, the game will appear to be Sweet Dreams Fuel, with pokemon happily living out their dreams of adventure by exploring the mystery dungeons; however, soon the Surprise Creepy kicks in, as they gradually discover signs that there are disadvantages to the Dream World making things real. Ultimately, they'll have to face the Big Bad's evil plan to corrupt the Dream World for its own ends...

The human from the second game is actually the future self one from the first game.
When time broke down, they were reverted to their human form, the canon partner for the first game was a Treecko who became Grovyle. Having saved the world once, they try doing so again, eventually traveling back in time, the player ending up in the same situation they did in their original adventure, but not knowing it. Also, they could be Gengar, who was the reincarnation of a human.
 * Alternately... If the protagonist is Gengar, who is still wanting to make up for his past actions, then Grovyle is the R/B player character (combining this with a guess seen above). No idea where this would put the R/B partner, but Gengar and Grovyle eventually started working together after.

The human from the second game is the alternate future version from the player of the first game
After the future was saved,the world had a happy history up until the point were the player character from Darkness/Time was born, only that the planet wasn't paralyzed and all. But another problem arose in form of the meteor, The higher power that Gardevoir worked for knew that the Player saved the world in an alternate timeline and thus he/she was chosen to save the world...again.

In the next Pokemon Mystery Dungeon game, there will be...

 * Pokemon from Pokémon Black and White.
 * A Big Bad that is an Expy of N, with his allies being of Pokemon that follow him.
 * Having two rival teams out of your guild, representing Cheren and Bianca. One will be strong against the protagonist, the other will be weak against protagonist.
 * Somehow become darker than the second game.

Any more ideas or if you wish to disprove me? Just add them in.
 * Rather than an Expy, N could himself be the villain.
 * Why would N/N-Expy be an antagonist? PMD already takes place where there aren't any humans. I guess it could work if the plot is to figure out what happened to the humans/reunite with them.
 * It will turn out Genesect is behind it all, whatever "it" is.
 * However, I'd like to add the suggestion that the villain could be human. Think about it. Be manipulating things from the human world and sending his Pokemon, serving as Psycho Rangers to the actual Guild the player is a part of, The Dragon, his strongest Pokémon, the fully evolved starter Pokémon with an elemental advantage over yours, acting as the Big Bad until his master is revealed, to do his plans in his stead, only coming to the Pokémon World after his Pokémon are defeated and arrested, taking on Pokémon form for the final battle. And in the end, it's revealed he's actually The Rival from the human world to the hero.
 * Or this human could be the one responsible for the human-less world, in order to make a Evil Plan to conquer the world. The human's name?

N is the ancestor of the Explorers hero.
However he/she ended up with the future crew, they're a human who understands Pokemon. N wound up passing the skill down.

N is the Explorers hero.
Though this kind of breaks down if you played as a female...

Possible starter pokemon for the fourth Mystery Dungeons and why

 * All the starter Pokemon from the normal games: It's kind of obvious.
 * Zorua: Ensemble Darkhorse.
 * Timburr: Decent stats.
 * Mienfoo: Female counterpart for Timburr.
 * Woobat: Type diversity.
 * Audino: Rule of Funny.
 * Deino: Rule of Cool.
 * Litwick: Type diversity.

The games take place inside the PC system

 * This is how your Pokemon keep themselves entertained when you're not using them - the other exploration teams are the player's other Pokemon, and the Wigglytuff Guild are the program. Normally, the system does its job pretty well. When a bizarre glitch appeared in the PC system, however, the player character was sent in to attempt a bug fix. However, the glitch interfered with the transfer, and the PC lost their memory and landed on the beach. This is also why there's a personality quiz at the very beginning of the game - it's preparation for the transfer, trying to make sure the PC is converted into a Pokemon that matches their battling style.

One or more of the kami trio will be the villain/s of the next Explorers games
It would probably help their reputation if they were actual, cool villains in the Explorers games.
 * Maybe both Tornadus and Thundurus could be villains. Then a big part of the plot could be to go find Landorus and stop them...

Team Skull is alive and well
After, you never see them again, but that doesn't have to mean they're dead. Alternatively they just left the Treasure Town area, having learned their lesson for picking on Pokepals and the Guild. They either found a new target or just decided to lay low and stay out of everyone's way.

There will be trainers you have to run away from in one of the games.
If you get caught, you have to fight all their pokémon. If they capture you, you have to play a minigame to break out of the pokéball.
 * Interesting idea, but it would never happen, considering that the Dungeon games take place in a human-less world.

How the PMD 2 protaganist got their power...
The Dusk Forest in the Future. Specifically, it is/was/will be Viridian Forest, and, as in Pokemon Special, it can grant people powers. And everything went from there...

Grovyle used to be human.
It's stated early on in Time/Darkness/Sky that the distortion of time is stopping pokemon from evolving. So how did Grovyle manage to evolve from Treecko? Answer: He didn't. He was turned into a pokemon as well, but never revealed it to his partner, as it was painful enough seeing them unable to remember him.

PMD4 starter guesses, courtesy of Bwburke 94
Water: Squirtle, Totodile, Mudkip, Piplup, Oshawott, Panpour

Grass: Bulbasaur, Chikorita, Treecko, Turtwig, Snivy, Pansage

Fire: Charmander, Cyndaquil, Torchic, Chimchar, Tepig, Pansear

Electric: Pikachu, Blitzle

Normal: Eevee, Meowth, Minccino

Fighting: Machop, Riolu

Ground: Cubone, Phanpy , Drilbur

Dark: Zorua

Psychic: Munna

Flying: Starly, Pidove

The Mystery Dungeons are games within the main series of games.
It serves as a decent explanation of why one series is so drastically different from the other. In the main games, virtually no Pokemon are sapient: the Pokedex has referenced Lucario and Lapras as being capable of understanding human speech, Alakazam's ridiculous IQ, and a few other hints of intelligence, but as far as gameplay goes, Pokemon are no closer to sapience than your average wild animal. It also explains ; outside of Mystery Dungeon, Darkrai is established as not being in any way malicious. Nintendo as a company does exist within the main series; the only reason Mystery Dungeon has never been brought up is because of the Law of Conservation of Detail.

The one asking you the questions in the Explorers personality quiz is
. This game repeats the first game's "This is the portal that leads to the world only inhabited by Pokemon". In the first game it made sense, since you're from the human world, but in this game, you're from the future. However, you did enter a portal to go back in time: The Passage of Time!
 * Um, yeah. This one's heavily hinted by the personality quiz music returning in a certain scene...
 * Plus, this could explain why.

The Pokemon are reincarnations of human characters.

 * Legendaries could be an aversion, considering they're generally immortal.
 * The hero is the exception to this: you were literally plucked from your time period, and turned into a Pokemon. As for why you could exist in the future, that's because someone managed to bring back the humans.
 * The single exception to all this would be Cyrus, since he'd still be in the Distortion World.
 * Gengar is likely Paul. After all, he's a jerkass and could've very easily The entire experience could be one big Ironic Hell for him. (Considering Gengar in canon, this isn't much of a stretch.)
 * Whiscash/Torkoal: Old Man Weedle.
 * Team Skull: The Team Rocket trio. Koffing = James, Zubat = Jessie, and Skuntank = Meowth. That's right!
 * Darkrai: Motherf****** GHETSIS!
 * Grovyle: ]

The player DID understand what Grovyle said...
...However, it was because of the Dimensional Scream. For me, it DID work in the future... Just in another way. After all, it is the dimensional SCREAM. Maybe it was used to talk with pokémon. Also, when Grovyle and the player talked with Celebi, she said that the Dimensional Scream couldn't be used to talk with pokémon in the past, and when the player lost their memory, it somehow remembered that part. That's why he was surprised when a Pokémon talked to him.

The player lost their personal memories, including the identities of Grovyle and Dusknoir, but not the knowledge or instincts they had picked up while in human form.
There is some pretty huge evidence towards this: they remember that humans can't understand Pokémon, they remain heroic just as they were in the future, and they generally seem like they stay just like they were as a human.

The titles of the first two Explorers games are Namesakes.
The titles may simply seem to be Rule of Cool, but they actually hide a deeper meaning; if you combine them, they can form the collective title of Pokémon Mystery Dungeon: Explorers of Darkness and Time (or Time and Darkness). This probably refers to the fact that later in the game, the player character.

Explorers of Sky simply refers to the mission in Shaymin Village, newly added in the remake.

The original Mystery Dungeon games occur in future!Oblivia
Future Oblivia collided with Hoenn due to shifting tectonic plates. This awakened the weather trio, who proceeded to destroy stuff. Due to this, the area was abandoned. My proof? Well while the islands potentially shifted around, stuff remained. Like the legendaries, the Latis, beasts, birds and Celebi, not to mention. Mt Freeze, Thunder and Blaze are Mt Sorbet, Layuda and Faldera respectively. The wireless tower fell to disrepair, becoming Mt Steel. The Pokemon are making the best of what is left of human technology.

Ghetsis is responsible for the lack of humanity.
Let's face it, if it furthered his goal, he'd take it. Wiping out humanity may have been an unintended side-effect, or worse, part of his plan. At some point, Ghetsis obtained a great power(the Creation Trio, Jirachi, ect) to kill all humanity, into a way that would reincarnate them all into Pokemon. Afterwards, he would use the disorientation and general lack of knowledge about human beings to conquer them all. Alternatively, it was a test drive in order to find a way to have total control of their minds.

Pink Celebi actually indicate gender, not shininess.
Or, to be precise, if a Celebi is shiny it means it's female. Yes, Celebi don't have a designated gender, but it could just mean gender unknown. This may go to explain why Celebi are so rare-there's only 1 female in over 8000.