Pokémon Gold and Silver/WMG

This page deals with Wild Mass Guesses for games and species in the Johto region. For non-game and non-Johto game WMGs, please refer to the appropriate page in the Pokemon WMG Index.

Wobbuffet's tail is its true body and vice versa.
That's the reason why it has eyes, why it tries to hide in darkness, and why it unleashes Destiny Bond when it's attacked.

The Unown are Hive Minded tools of the primal forces of order.
As opposed to the unknowable Eldritch Abomination that is Missingo, the Unown are the living tools of an unfathomable force that manifests itself as writing - the essence of knowledge and law. When alone, they are weak but capable of developing independent personalities. Together, they are incredibly powerful. They seem to be attracted to ancient ruins, and even the greatest minds of the Pokemon world are unable to fathom their true purpose...
 * So, they're an independently individual version of the Auditors, minus the genocide?
 * "Minus the genocide"? What do you think their true purpose IS?
 * So, wait. Since Santa exists... Oh man. That's evil!
 * On the other hand...

The Unown are the Language of the Universe
Coinciding with the above WMG. Unown are weak individually, but together, they have great reality warping capabilities, as shown in the 3rd movie. And in the HG/SS Arceus event, Arceus uses a bunch of Unown to create a Dialga/Palkia/Giratina out of nothing. Or rather, to reprogram reality so another can be born. It's even possible that Arceus used the Unown to create/shape the universe in the first place. So, a being with enough power and knowledge could potentially use them to rewrite reality to their whims. The ancients in the Ruins of Alph were aware of Unown's power and based their language on them in an attempt to tap into that power.
 * So they are truenamers? At least it explains why they suck so much.
 * This would actually imply that Unown were the first Pokemon in this universe, and probably created Arceus out of boredom. Then they helped Arceus make the universe. Seems reasonable enough.
 * The architect of the above theory proposes some addendum: in the third movie, on indulging the whims of an upset little girl they could create anything she desired. But they're often seen in the company of the creator of the universe... are these the tools of the Gods?
 * "In the beginning was the Word, and the Word was with God, and the Word was God." It makes too much sense not to be intentional somehow.
 * So Arceus is essentially the collective consciousness of the Unown?
 * Alternately, the Unown are the "thousand arms" of Arceus. The mythology surrounding the creation of the world was merely metaphorical.
 * Fridge Horror: If the Unown are part of Arceus, it means that the Team Rocket radio signals likely screwed around with the mind of GOD.

Will is a girl in disguise.
Or at least a hermaphrodite, I don't know. Proof? [http://archives.bulbagarden.net/media/upload/1/1b/HGSS_Will_Art.png Look at these hips. These girly hips.]
 * And his team in the remakes is all female. Hm...
 * I see him as a trans* guy.

Jasmine is from Sinnoh.
Not only do you see her at Sunnyshore City in D/P/Pt, she also participates in Super Contests. The reason she says Sunnyshore reminds her of home is because Olivine is where she moved, but she was born in Sinnoh. That, and her last Pokemon in the HG/SS rematch is Empoleon.

Jasmine and Caitlin are Sisters.
First of all, just look at the two of them. Both of them have long brown hair. Both have similar builds and dress in the same style outfit. Both seem to have a streak of shyness running through them. Also, it would explain why Jasmine was in Sinnnoh during D/P/Pt, visiting her sister; the same goes for Caitlin in Johto along with the rest of the Frontier Brains in HG/SS. Also, Jasmine in general seems to be somewhat of a doer of good deeds. If she came from a rich family, she would have the money to help out like that.
 * Must be some wealthy family, given

Baoba makes Ethan/Lyra the owner of the Safari Zone as a tax dodge.
Building a Safari Zone has to be a huge financial undertaking. No one would hand something like that over to anyone for free, much less a little kid, unless there was some subversive reason. And as owner, you never see a single dime of profit—it all still goes to Baoba. Hell, you still have to pay to enter!!! The "test" he gives is just a meaningless little thing to make a naïve 10-year-old think they've earned it.
 * This is actually much more believable than the in-game explanation.

Silver is 14 - 15 years old.
A guy mistakes Red for him, who was eleven in FRLG. How could they mistake a 7 - 8 year old for an eleven year old? Possibly, Lyra and Ethan are that age too (they seem the same age as him). Also, possible back up, their heights and weights.
 * Um, Silver is supposed to be around 11, and since the game takes place 3 years later than FRLG, Red would be 14.
 * Yes, that's what he's saying. The guy in question is in the Kanto remakes, when Red's eleven and Silver's eight or so. In the sake of fairness, Silver uses the same sprite in the Giovanni event (where we see him right after Red beats Giovanni the last time), so maybe he's just mature for his age? Or the guy in question didn't know much about Silver besides his hair color? He would also mistake Leaf for him if you played as her.
 * Silver has no stated age, just like everyone else. What I meant was, they mistook a supposed 7 -8 year old for an eleven year old. If he has seen Silver and recalls him well enough, that seems unusual unless Silver is Red and Leaf's age. Taken from that, Lyra and Ethan are Silver's age.
 * Actually, several characters do have confirmed ages (Rowan and Cyrus are 60 and 27, respectively), but never mind that. The exact quote that the scientist says is "You... You're not Giovanni's kid, are you? No, that can't be right. Giovanni's kid has red hair." That doesn't really say whether or not he's met or even seen Silver; for all we know he could have just assumed the player character was Giovanni's child who had come looking for his father, and then remembered somebody telling him the kid was a redhead. There's really not enough info to say what exactly the case is, it could just be a continuity error.
 * The quote could be referring to the fact Red is frequently mistaken for Ash, and the theory that Giovanni is Ash's father.

Silver's mother is either Rocket Executive Ariana or Lorelei of the Kanto Elite Four.
Think about it, his red hair has to come from somehwere, and both of them have a very similar shade. So, I'm guessing that the situations could have gone like this:
 * Ariana: he was the result of a one night stand, where neither Giovanni nor Ariana had any intent to have a real relationship. Then, Ariana got pregnant. She didn't want the kid, not being very well off, but Giovanni said he would take it and raise it on his own, excited about the prospect of having an heir to his title as Viridian Gym Leader and as the Boss of Team Rocket, while the organization was still in its infancy. So when Silver was born, Giovanni became his legal guardian and Ariana left. Later in her life, Ariana regretted not being a part of her child's life and joined Team Rocket in an attempt to get close to Giovanni and re-enter Silver's life. While she was exceptional at battling and quickly rose up the TR ranks, Giovanni resisted her advances. Later, in GSC and HGSS, she's still attempting to impress him, thinking reviving and leading the new TR would make him interested.
 * I believe Ariana is the mother, because "Ariana" means "Silver" in Welsh. I don't think that was an accident... And the hair is more red while Lorelei's is more orange, plus the hairstyle of Ariana resembles Silver more.
 * I don't think it was simply a one-night stand. Giovanni felt that Team Rocket may one day need an heir. Due to being good friends, Ariana helped him get his son. They may even be lovers, but their relationship is secret(Giovanni doesn't want to ruin his Villain With Good Publicity angle). Their relationship has likely been soured and broken after Silver left the group.
 * Lorelei: they actually had a relationship, Lorelei being attracted by Giovanni's power and skill as a Gym leader (she probably wasn't E4 yet) and rugged good looks. Giovanni was also impressed by her skill and thought she could make a vital difference in Team Rocket (once again, still a young organization), and perhaps also be a good girlfriend/wife. After Lorelei became preganant with Silver, Giovanni thought it meant he finally had the hook he needed to pull her into Team Rocket, and Revealed his plans and intentions to her (as she didn't previously know about his TR involvement), hoping it would make her more attracted to him. Needless to say, this backfired; instead, she was disgusted that he was a budding crime lord, and that she had fallen for a man so evil. She left him, and when Silver was born, not wanting the reminder of her involvement with him, she left him on his gym doorstep. Giovanni took the advantage to start raising a heir to Team Rocket, the son of two great battlers.
 * With Ariana, I've always thought that it was a sexual-only affair or one-night stand when she was in Team Rocket, maybe a grunt or young admin. They are a mafia, so that wouldn't be much of a stretch.

Silver is the player's half-brother.
Notice how your mother has brown hair, like Lyra, but where does Ethan get his hair color? The only important people with dark hair are Bruno, Koga, Giovanni and, uh....Yes. Plus, when you meet Petrel, he comments "Hmm, you're saying I don't look like Giovanni," or something to that effect. Either Giovanni is a wanted criminal (likely) OR he's the character's father, and he broke it off with your mother. No one brings it up because it seems mean to point out that your father is a notorious criminal.
 * Probably it's because Giovanni is a well-known criminal. He's a dangerous man on the run, and during the Celebi time-traveling event, Ethan or Lyra both know who he is and that he's the Rocket boss on sight.

The Kimono Girls are a heroic secret society working behind the scenes for a better tommorrow.

 * ...Dude. It all makes sense now...
 * I thought it was just the opposite: They we an ancient pagan cult manipulating you to bring back their god. And they were using you to bring it back, regardless of your safety.
 * They're part of an Ancient Tradition worshiping powerful and potentially dangerous beings, but in the least harmful way possible. Lugia or Ho-oh probably wouldn't hurt a human, at least not in a regulation battle: Ho-oh is explicitly more about bringing the unjustly and accidentally killed Back From the Dead than about killing a human (see the Legendary Beasts' origin story), and while Lugia's only characterization was in the movie (which happened during a Filler arc that lies completely outside the games' canon), we can assume it's not an evil or violent being either, at least not intentionally (it was a different story when Cipher got their hands on it, but let's not go there.) Both are capable of being destructive, as are the Legendary Beasts who tie into their story, but none of them would harm you unless they were cornered. After all, Pokémon is pretty damn idealistic outside of Colosseum and XD. The Kimono Girls want humanity to see Lugia and Ho-oh again because of the good effects they might have. I think the line in Crystal talked about the hearts of humans and Pokémon communing? And there was that stuff in the Ruins about walking with Pokémon in harmony. They probably believe that Ho-oh and Lugia will make humans kinder to Pokémon, and possibly to other humans. Remember, HG/SS take place during and just after Diamond, Pearl, and Platinum, as evidenced by . The story got out about Cyrus, as Cynthia (a Champion, unlikely to lie) and the remaining Galactic Executive (who could provide secret documents, etc.) had probably told the media about what happened. The Kimono Girls decided the time was right to bring back the Legendary Birds and improve the lives of humanity. After all, we never know when the next Cyrus will emerge, and there won't always be a 10-year-old kid running around who can capture Palkia/Dialga/Giratina... Oh, look, a 10-year-old kid who can probably capture Lugia and Ho-oh and all three Legendary Beasts!
 * The games have shown both Lugia and Ho-oh are good Pokemon at heart. Ho-oh revived the beasts and shows up in Colosseum to stop the big bad from escaping, and Lugia sealed itself away because its power was too dangerous (and ended up corrupted in XD, so that means it can't have been evil to start with).

Johto is a post-apocalyptic wasteland.
Think about it. The Kimono Girls are manipulating you to bring back their god, possibly to have it repair the damage to the land and revive the dead. (The three legendary dogs gave them this idea.) This is in HG/SS, so maybe the apocalypse happened recently. The Kimono Girls are pretty straight-forward, but let's analyze the rest of the land and make educated guesses.

Tin Tower (where you meet Ho-Oh) features advanced technology in panels. Yet, most of the tower is old and run-down. Why are the floors so complicated and maze-like? To keep the unworthy from reaching the top? Or was it being rebuilt? Did something happen to destroy most of the inside and the monks had to rebuild?

How come there aren't a lot of roads connecting around towns and cities? Take Ecruteak: to the west, bumpy paths and grass. Makes no sense, the way it's designed. To the South, a patch of grass, making people who have no Pokemon unable to get to Ecruteak. Either the Gym Leaders did this (see below), the townspeople became paranoid of other people and isolated themselves by destroying the roads, trade relations broke down, or some horrible natural disaster wiped away the roads and lands.

Proton killed the mother Marowak.
It fits his Psycho for Hire, Combat Sadomasochist personality. It took place around, or a bit before, RGBY/FRLG and he looks no older than twenty five so he should have been in his late teens - early adulthood. If Ariana and Archer were admins during that period, why not him?

Youngster Joey isn't a Youngster.
Rather, he's a Rich Boy, disguised as a Youngster. The evidence would be his Rattata, which, if one hacks the game code, has maximum IVs, something that can only happen through extreme luck, or complicated and extensive breeding (which would likely be too expensive for a Youngster to afford). Why he's disguised as a Youngster could probably be greed- losing trainers have to give away half of their money, which is signifigantly less for a Youngster than a Rich Boy.
 * Jossed: That Max IV's crap is fake.

Ho-oh turned Kris into Lyra
Somehow or other, Kris was horribly injured and near death(if not dead). Ho-Oh happened to be in the area and revived her... though if indeed the Legendary Beasts were once Eeveelutions, then it's reasonable to assume that humans revived by ho-oh would change as well, both physically and somewhat mentally. (Also, this is most definitely how it should have happened in the manga.)
 * ... this is a semi-crossover wmg isn't it?

Victini caused the destruction of the Brass Tower.
It was, in fact, created to be used in some ancient war between Poke-Pan and Unova, and proved to bring a swift victory on its first use. Because of its power, Victini was locked away, never to be used again in battle (until you come along). The people of Ecruteak City simply mistook its horrendous attack of pure blazing fury for something just as fast and just as fatal: a lightning bolt.
 * ...too soon, man.
 * Too soon? When would the first hostile use of a weapon capable of murdering civilization ever be allowed to be taken lightly?! This'll be in bad taste until humanity has ended.
 * Wait, I just realised that Slateport City is based of Nagasaki City...where the second atomic bomb was launched. DAMN YOU VICTINI! DAMN YOU!

In the second generation, baby Pokemon weren't really newly discovered.
They just hadn't classified them as a separate type of Pokemon. Before that, they just referred to Magby as a baby Magmar, Elekid as a baby Electabuzz, etc. After much scientific debate, they changed it.

Falkner's Father is Koga
Because wouldn't that be hilarious? Having him and Janine have a 'War' over their fathers without knowing its the same man? His promotion to the Elite 4 was a blessing, since it right between both his kids. How does he lead this double life? Ninja Powers obviously. Plus, Look at his Main Pokémon, Crobat. Poison AND Flying typed.

Pryce's after battle quote is a metaphor
"When the ice and snow melt, spring arrives. You and your Pokémon will be together for many years to come. Cherish your time together!" The ice and snow is a metaphor for Pryce's life. He is old and acknowledging that his death is near. He's telling you to cherish your time with your Pokemon because, in his old age, he's seen many of his own Pokemon wither and die. He's just an old man who is satisfied with his life and is ready to die.

Whitney has a Southern Belle accent
She does have a dialect in the Japanese version (Osaka-ben I believe) but no translation has showcased it. The games didn't give Bill an accent in the translation so who knows what Whitney has.

If the protagonist of these games are ever stated it'll be Lyra
The female protagonist is showcased in multiple official artwork, Lyra looks like Red (which would make the "your eyes look like his" dialogue people say throughout the game a double meaning), and it'd give a ratio of one male canon protagonist and one female.

Archer is related to Cyrus.
Sounds like "Wild" Mass Guessing indeed at first, but there are a few reasons this could work. First, they both have similarly-colored hair, and people often use hair in the Mars-Ariana-Silver-Roark family guess. Secondly, as just mentioned, this isn't the first time someone's guessed that Johto and Sinnoh characters could be related. Thirdly, it's commonly accepted that Johto and Sinnoh take place at similar times; in Platinum, Cyrus is confirmed to be 27, and Archer at least looks like he's about early-to-mid 20's, so taking their likely-similar ages into account, they could very well be siblings/cousins.

Oh, and they both have a Houndoom. Although Cyrus only has one in Platinum, not Diamond/Pearl, but Platinum is generally taken as the canon game anyway.

The two unnamed people in Olivine Gym in the remakes are part of Jasmine's family
She's too shy to have taken on Junior Trainers. Based on their appearances, I'd guess they are her younger sister and her grandfather.

Red died after losing to Gold/Ethan/Kris/Lyra.
Red trained at Mt. Silver for three years. The shame of losing to someone who first became a trainer about a month ago caused him to commit suicide. The screen blacking out was just to hide that he jumped off Mt. Silver in shame. This is further supported by the remakes, where Red is standing right next to the edge of the top of Mt. Silver.
 * How do you rebattle him, then? I know what you're going to say...
 * The same reason the Elite Four acts like you haven't challenged them before, even though you've beaten them 10 times. The battle with Red only happened once canonically, it's just that you're allowed to relive those events just before his suicide.
 * You (the player character, not the above troper) are sick. Fighting a suicidal trainer over and over, with him jumping off the edge of a cliff (or being knocked off the edge of the cliff thanks to the shock of losing) every time you win? Unless you (the player character) think you're actually traveling to the past and can change his mind... *shudder*
 * After becoming Champion, Red defended his title against an endless wave of challengers. He gradually lost his enthusiasm for battling, and eventually surrenders the title. He sought the ultimate challenge, hence his journey into the heart of Mt. Silver. (Assuming that legendaries only show themselves to those who are "worthy", Red in his glory-seeking mental state is hardly fitting.) Eventually, he reaches the end, when he realizes that he has conquered the toughest challenge for any trainer, and prepares to leap off of the edge when the player character walks in...
 * No. He didn't die, he blacked out. He is still mute since he was a Silent Protagonist, so it would make sense that he would do what he did in RBY when he lost: lose some money, black screen, fade in to the pokemon center safe and sound. By the time you get back there, he had already Flown away.
 * He never died and as previously mentioned, blacked out. This is even mentioned by Green after you defeat Red, congratulating you for doing it. Implying that they met up after he got beaten

R/B/Y and G/S/C are an alternate continuity - but not originally.
Unforseen messing around with the time machines Bill invented (possibly involving MissingNo.) corrupted spacetime. In order to prevent the corruption from spreading to the rest of the series, Fire Red and Leaf Green retconed them, thus quarantining the corruption (and, perhaps coincidentally, perhaps not, MissingNo.) and splitting them into their own parallel universe. ''Ph'nglui mglw'nafh MissingNo. G/S/C wgah'nagl fhtagn''.

Sabrina went to space between the events of RBY and GSC.
In Ruby/Sapphire/Emerald, there is a space station that is virtually unused. Yes, Team Magma raids it, but I don't think that's all there is to it. Gamefreak weaves masterful plots, and I doubt they'd let the space station go unused in the grand story of Pokemon. I believe in the three year gap between RBY and GSC, Sabrina boarded the space station, and went to space. There, she met some friendly aliens. Sabrina was in a tsundere relationship with the aliens, due to her strict and down-to-business personality. However, Sabrina became a Defrosting Ice Queen, and became more easygoing, as seen by her choice of attire in HG/SS, such as the slutty outfit and the space bracelets (which is the smoking gun of the theory) In the RS 3DS remakes, we will see Sabrina boarding the space station to meet the aliens.

Misty joined Team Rocket in the three year time span.
Proof for this? Talk to the Rocket Grunt in front of the Radio Tower. Notice how she calls you pest. Misty frequently calls you pest when you meet her. That's the real reason why she's annoyed at you; is because you ruined Team Rocket's plans, not because you interrupted her date. In addition, the Rocket grunt sprites have red/pink hair. Misty has red hair too. I fully believe that in the 3DS remake of Fire Red/Leaf Green, they'll reveal that Misty was part of Team Rocket all along.
 * Adding to this: Not only do you fight a Rocket Grunt in Cerulean City in the Kanto games, in the Johto games the last Rocket Grunt hides the Machine Part in the gym and then decides that the bridge right next to town is a great hiding place. Putting the Machine Part in a gym means it would have to be noticed eventually and would normally be a stupid move... unless he had reason to believe that Misty would help him hide it.

Bill's Time Capsule in Gen II messed up the timelines, which resulted in the events of the remakes.
It explains any and all differences between the remakes and originals. It's also why the later games are incompatible with the older ones. Alternate timelines and all.

Misty's "boyfriend" that she refers to in Silver/Gold/Crystal/SS/HG is really Ash (Red)
Her boyfriend was "late" or whatever, but really her "boyfriend" is Ash(Red) who is obviously up on Mount Silver. She wasn't waiting for a date, nor where they actually a couple, and she was there because she was sad because she still loves him and was depressed, wanting to be alone.
 * Ash and Red aren't the same person. Red came first, then the anime and Ash.
 * Wait... she said he was "late"??? Oh my god, Red was a ghost! That would explain why no one talked about him in the other games, other than "You remind me of...

Cinnabar Island did not erupt
It was dragged into Glitch City by Missingno's influence. The only reason the island exists at all is because only the town and the volcano were sucked in, somehow sparing the Pokemon Center. Blaine survived because he was probably off the island at the time. Why? I dunno.
 * I bet Blaine knew about Missingno and tried to create a countermeasure. It saved the Pokemon Center and everyone inside it.

The eruption on Cinnabar is your fault.
"It is said that when it roars, a volcano erupts somewhere around the globe.
 * When you're in Ecruteak, you're forced to awaken the Legendary Beasts to progress with the story, correct? And when they wake up, they give a yawn of a roar. But check this:

Entei's Pokédex entry, Diamond/Pearl/Platinum"


 * Entei roars, volcanoes erupt. Entei roared when it woke up, before running off, and... Well, by the time you get to Cinnabar, all that's left is the Pokémon Center. No humans died, but the Pokémon in the mansion? Probably dead. All the buildings and property on the island? Hope they had insurance. Anything they were researching at the lab? Gone, along with all record of its existence unless they had a backup somewhere that wasn't destroyed. It was almost a year before you get there, but the period between the end credits following the defeat of Lance and you finally making it to Kanto is never necessarily detailed now, is it?
 * Alternatively, this could apply to any Entei-related incidents post-FR/LG. Red could be walking to Mt. Silver two years later and run into one, it gives out a battle cry, Cinnabar erupts.
 * It was your fault, but there was nothing you could do to prevent it in the first place. Eusine and Silver were already looking for the legendary dogs. They would have found it eventually.
 * ...Cinnabar erupted two years before the protagonist became a trainer.
 * Cinnabar was already destroyed, but there's still Mt. Chimney in Hoenn. You inadvertantly completed Team Magma's evil plan!
 * Except Team Magma's plan was stupid. Assuming you made Mt. Chimney erupt, all you probably did is grant Lavaridge and potentially Fallarbor Town a horrific molten death

Lt. Surge put the Snorlax blocking the Diglett Cave in GSC
He was tired of being owned by every challenger who had a Diglett/Dugtrio. Because, really, Poor Predictable Rock is one thing, but living right next to a nest of your weaknesses makes you Too Dumb to Live.
 * In B/W, almost ALL the Gym leaders live next to their weaknesses. Maybe it's the league rules...
 * Considering B/W takes place in a simile of America, and Lt. Surge is blatantly and canonically American... Maybe he's just used to the old rules!
 * Diglett have incredibly low defense and electric types are extremely fast. Gameplay aside, Surge shouldn't mhave had much trouble beating any diglett users that came his way.
 * It's a plot point that he evolves his Pokemon for power, not strategy, but the overconfidence would fit with his characterization.
 * That about evolution is Anime-only

Kanto and Johto are more polluted than the other two regions.
Hence why there are more Poison-types in both regions. The game even says outright that a pond in Celadon City is polluted with Grimer. Also, there are more Grass/Poison Pokemon there, either because they feed on polluted water (notably, good places to find Oddish and Bellsprout are near the Power Plant and Cerulean City) or because they developed the Poison-type as a protection because Grass-types are otherwise easily poisoned.
 * Well, it would explain why berries don't grow there... at least, not anymore.
 * Perhaps Apricorns are hardier than the old Berries which is why they can survive?
 * Berries resemble tomato plants, which are small, while Apricorns grow on trees, which are much hardier than smaller plants.

Bill is a member of Team Rocket Bill and Giovanni are the same person.
A random civilian in Cerulean City mentions that Bill's not "above doing all sorts of things to get rare Pokemon". Sounds a lot like Team Rocket. Also, note that Bill loves rare Pokemon, but he lives a hermit-like lifestyle, not even going on a cruise party that has sailed around the world. It's not that Bill doesn't like people, it's that he's afraid that there may be someone who has beaten him in the Viridian City Gym and might recognize him. Also, note the lone Team Rocket member who steals the Dig TM. He could be working as a free agent, but it's much more likely that there's a superior agent nearby. But what really kicks it is when Bill fuses himself with a Pokemon (A Rhydon or something similar in R/B, a Clefairy in FR/LG); after Bill is returned to normal, he never speaks of the Pokemon again.
 * In Gold and Silver, once Team Rocket is actively searching for Giovanni, Gold/the player only sees Bill for incredibly brief periods of time; and he always seems to be in quite a hurry, mostly communicating through in-between agents and screens.
 * This brings up the question of how he knows when to return to the gym. Very simply, Old Man Weedle is acting as his eyes and ears, warning Giovanni/Bill ahead of time when a trainer powerful enough to face him is coming so he can quickly Fly to Viridian and fix the Broken Bridge unlock the Gym.
 * He has a video camera in the door of the gym, or some sort of scanner for the number of badges a player has. He then uses the teleporter to get into the gym. The "broken teleporter" story is just a case of Obfuscating Malfunction, so that people assume he can't get to the Gym on (literally) a moment's notice, and that he has nothing to do with those working teleporters Team Rocket has.
 * In the anime, his door has an image of Mewtwo, at a time when the only people who know about him are the scientists who made him and Giovanni. Which would imply that Bill is either a high-ranking member of Team Rocket, or one of the scientists involved in the creation of Mewtwo.
 * Using the anime as evidence for the games? Really? REALLY?
 * Likewise, the only way to get to his cottage is by traveling over Nugget Bridge, which is guarded by a Rocket grunt.
 * Speaking of Nugget Bridge, a guy in the Cerulean Pokemon Center in FR/LG comments that Bill will do whatever it takes to get rare Pokemon, and he's "not above doing all sorts of things." Sounds a bit fishy in light of this theory.

Giovanni killed himself after Heart Gold / Soul Silver.
All we hear after he leaves after the battle is a splashing sound.
 * Or that could be radio static.
 * Jossed. Giovanni will appear in Black 2 and White 2.

Red is still the Indigo League Champion when you fight him.
However, because Red is so young, Lance is the acting Champion - kind of like a regent. It's not clear if the GSC protagonist is now the Champion after beating Red at Mount Silver; does it count since they weren't at the Pokemon League?

Red and Gold/Ethan are brothers after all.
Well... all we know is that they have different moms. Red and Gold are related through their absent father. Because obviously two insanely talented preteen Pokemon trainers can't exist in the same game and not be related to each other in some way.
 * Well, Gold/Ethan's Expy-of-Red status was pretty blatant back in GSC, until FRLG and HGSS differentiated them a bit more... Given how much they used to look alike, this is fairly plausible.

Ethan looks like Red because he copied Red's style.
Ethan spent his childhood watching the tv broadcasts of the Pokemon league fights and hero worshiped the champion. So, to be more like him, he wore similar clothes and got a similar haircut.
 * It's only been 3 years though. His hair isn't even that similar to Red's.
 * Well, not anymore, but it was slightly more similar in their original artwork. At least it was the same color, anyway.

Giovanni wasn't the head of Team Rocket
According to Bulpapedia "The official Red and Blue guide from Nintendo Power, Giovanni was labeled to be a regional boss of Team Rocket" My guess is that in Red and Blue Giovanni planned to take over all of Team Rocket. But Red managed to stop him for reaching his goal.Come Gold and Silver a few rouge members of Team Rocket are trying to build a regional version of Team Rocket in Johto some of the higher ups in Team Rocket caught wind of this and they decided to use Gold to stop them from growing too strong by using Elm to act as a Pokémon professor(how else do you think he got the starter Pokémon?), because they are shown to have a mass following and just needed Giovanni to kick start things and the Celebi event tells you he was ready to rejoin them. Team Rocket is most likely still around.

Cameron the photographer is a former Team Rocket member
He was most likely a recruiter for the Rockets prior to their inital disbandment, whiches explains why he has alot of spare team rocket uniforms, and when ever the player rejects the option of having their photo dress as a Team Rocket Grunt, the reason why he say "yeah nobody should dress like Team Rocket" is him rembering his dark past and when Team Rocket was serious business and when impersonating a Team Rocket member would of gotten you either arrested by the police, killed by the Rockets themselves or even getting recuirted by the Rockets becoming a Rocket for real. And when team Rocket took over Goldenrod City Cameron either fled so that he would not be hunted down and killed by his former comrades or got in his old uniform and hid himself amongst the Grunts until the player defeated Archer

Red and Leaf are the same person
It could go either ways: 1. Leaf is crossdressing as Red. 2. Red is Transsexual, began his journey as Leaf, and transitioned sometime inbetween FRLG and HGSS.