Iron Chef/WMG

Chairman Kaga is a Diabolical Mastermind.
Ever wonder why we never see any of the challengers again? If they win, they are abducted and mind-wiped, and they become a minion of the Gourmet Academy, ready to move against the world with their superior cooking skills. If they lose, they become the next battle's theme ingredient.
 * And what is the source of Kaga's power? Yellow capsicum. That explains the evil grin when he bites into the capsicum in the opening credits.
 * OK, then why does it look like he's choking on it several seconds afterward?
 * For the same reason Popeye in the Robin Williams film of that name dislikes spinach. Just because it's the source of his power doesn't mean Kaga enjoys it in itself.
 * No, he's holding back a diabolical laugh. Laughing diabolically and eating at the same time can lead to choking.
 * The Ohta Faction challengers that lose aren't seen again in subsequent Faction-related battles. This is explicitly pointed out by the commentators. Coincidence?
 * Further note: Morimoto's first Faction challenger was seen again for one further battle. He was in the royal box during the third Faction battle, but he was never seen again in Kitchen Stadium after that. After this was when the commentators started noting the disappearances, with a Hand Wave that they were "banished" from the Faction for losing. But they couldn't have been "banished" after losing if the first Faction challenger showed up again as a Faction member!

Chairman Kaga is a vampire
He likes poofy shirts. He cannot swallow the capsicum, but intstead appears to gag; perhaps he cannot eat solid food at all.

Losing challengers are never seen again. He drains them dry.

Also, he gets subtitles instead of being dubbed into English. This is because he hypnotized whoever is in charge of the dubbing so that no one spoke the Black Speech in English.

Chairman Kaga either swore off drugs or started taking the right ones
Seriously: Watch some of the early episodes (the ones with Michiba as IC Japanese). The man was seriously tripping off something. The Kaga we know and love is a dignified Large Ham. The early Kaga was a manic-depressive madman who wouldn't sound out of place yelling, "The theme ingredient is... ORPHANS!"
 * Chairman Mark could take an example from his uncle.

Yutaka Ishinabe, the original Iron Chef French, was eliminated for trying to rebel against Kaga's mad rule.
Consider: when he rose into Kitchen Stadium, he was holding a capsicum, Kaga's trademark. Clearly, he was signaling his desire to steal Kaga's power. In his last battle, the only one he ever lost, Kaga "accidentally" gave away the theme ingredient a little early. Kaga was setting The Starscream up for a fall.

Yutaka Ishinabe is being retconned.
Beyond several 'honorary' cameos and a blink-and-you-miss-it spot in the opening credits (check the wall behind Kaga), Iron Chef Ishinabe has pretty much disappeared from Iron Chef canon. A highlight special made for American audiences featuring Iron Chefs Hiroyuki Sakai and Chen Kenichi outright claims that Sakai is the first Iron Chef French. Food Network and Fine Living Network have only shown one of his matches, the only one that he lost, noted above, as opposed to Food Network showing several of Iron Chef Japanese I Rokusaburo Michiba and Iron Chef Japanese II Koumei Nakamura's battles. (Fine Living, not so much.) This smacks of Retcon.
 * This WMG and the one above go hand in hand. Kaga set Ishinabe up to fall, and then he tries to erase Ishinabe from Iron Chef history. This is made easier because Ishinabe only participated in eight battles. But Kaga can't wipe out everything because of that darned portrait, and so a few cameos remain.
 * Wouldn't it have been easy to complete the Retcon by refilming the small amount of the opener that had Ishinabe's portrait in it, though? Or was Kaga being lazy or wanting to bask in the glory of vanquishing a rival?
 * Kaga didn't remove Ishinabe from the intro because he is totally inept at Photoshop.
 * Ishinabe does appear in one episode, filling in for Dr. Hattori when Hattori was a challenger. Kaga did it just to rub Ishinabe's powerlessness in.

The real Chairman was the psychic judge they had on, Kazuko Hosoki
If you think about it, the Chairman should only show up sometimes to test how it's going and wouldn't be on every episode.

There was no clear reason to have a psychic on a cooking show. There must be something sinister involved!!!!!!1!1!oneoneone
 * If Hosoki were Chairman, then there would be a mutiny. There were times during tasting when she's been a complete and utter bitch. No...

Yukio Hattori, the chairman of a nutrition college, is the real Chairman of the Gourmet Academy.
Think about it for a bit. The commentary booth is the perfect place to monitor goings-on. And the only time Hattori had to serve in "official" capacity as Chairman was when Kaga "boycotted" proceedings because of a losing streak.

Chairman Kaga faked his death by fugu poisoning.
When the 21st Century battles were held, Sakai and Morimoto lost their battles to their longtime rival and an American upstart respectively. Having lost face so publicly and in such important battles, Kaga faked his death so that he could disappear for good. He was only brought out of his self-imposed exile when his nephew approached him with the plans for Iron Chef America, and then only to give his blessing (a blessing his other nephew, who tried to continue Iron Chef in Japan, sorely lacked).

Chairman Mark is also a Diabolical Mastermind, and Alton Brown is The Dragon.
Okay, this is part Rule of Cool here. But Chairman Mark could have pulled a page from his uncle; perhaps Diabolical Mastermind-ness runs in the Kaga family. And Alton Brown certainly holds a lot more power than Kenji Fukui ever did, and is on equal standing with the Chairman.

Alton Brown is the true chairman of the American Kitchen Stadium.
Alton Brown DOES hold a lot more power than his predecessors, and he is credited with hosting duties in the credits. (Mark Dacascos isn't even IN the credits.) It's possible that he was the one to revive the Gourmet Academy; he placed Mark as a figurehead to give Iron Chef America some credibility.

More telling evidence: You would think the Chairman would be heavily involved in The Next Iron Chef, since whomever wins becomes his newest minion Iron Chef. But all the supervising and overseeing is done by Alton Brown. Hell, in the second season, Chairman Mark isn't even at Kitchen Stadium, having been detoured into the Dancing With the Stars studios; he relays his messages through video.

One of the American Iron Chefs is leaving.
The first Next Iron Chef competition was held because Mario Batali had left the Food Network over a contract dispute. The Food Network just announced a second season of The Next Iron Chef. Presumably, this means one of the current Iron Chefs is leaving. We don't know who, but three of them have good reason to:
 * Bobby Flay is spread too thin among Food Network shows and his restaurants; he may have chosen to quit ICA to prevent burning out. Or possibly there's another contract dispute.
 * Morimoto may finally be fed up with being an Iron Chef. Remember, he served under Chairman Kaga as well.
 * Cora has reason: both she and her partner have had their second respective child, and she might be taking a maternity leave to spend time with them.

It isn't Michael Symon!
 * The case for Morimoto has weakened: he's appeared as a guest judge in the most recent episode.
 * Based on the preview for the final episode of The Next Iron Chef, it looks like Cat Cora will be the one leaving.

Alton Brown appealed to Chairman Mark's pride or honor to attempt a Uriah Gambit-cum-Xanatos Roulette and gain unquestioned control of the show.
It has just been announced that Chairman Mark is on Dancing With the Stars (American vs.) this season. Anyone who has watched recent seasons of that show know that, underneath the heartwarming vignettes and beautiful moves, it's a blood sport -- both contestants and pros get injured frequently. They are encouraged to stay in while injured. (Last season, two "dances" had to be judged via rehearsal footage.) In short, it is one of the few competitions even more dangerous than Iron Chef.

So, Alton Brown appealed to Chairman Mark's honor and got him to want to be on that show. The object is to supplant Mark. Ideally, Mark will be so badly injured that he will be unable to do his job ever again. There is also the possibility that he will be kicked out of the Gourmet Academy because he's been away for too long -- Dancing With the Stars takes six weeks plus however many weeks he can stay in the competition (it's live!). Alton will then seize control, perhaps placing another figurehead in the Chairman slot.
 * That is awesome. The only way this WMG could get better is if it doesn't go just as planned and Chairman Mark comes back and puts Alton in his place.
 * Oh no, Brown is a TV chef. It's in his nature to always prepare things ahead of time.
 * Yeah, but chances are there's some sort of Spanner in the Works. No clue what yet, but it's out there.
 * It appears to have failed so far. Chairman Mark kept taping for Iron Chef even while he was rehearsing for "Dancing," and he came out unharmed -- though his professional dancer-partner Lacey Schwimmer got hurt twice! The first time was a muscle pull; the second time was, apparently, a Ki Attack that Mark deflected that then hit Lacey. (He tells her, "Go home!") Chairman Mark just got voted out, so he may come roaring back to Kitchen Stadium yet.
 * Alton Brown is accused of being a Time Lord. Chairman Mark is accused of being a Time Lord, albeit a regeneration of Chairman Kaga. Perhaps this was one of many ways Alton tried to get the upper hand against Mark in an ongoing battle between the two of them, and their relationship is less-for lack of a better analogy-Doctor and companion and more Doctor and Master. Minus the Foe Yay.
 * Oops. Chairman Mark is (as is custom) appearing on the Dancing With the Stars finale. Alton must have done some fine manipulations: Chairman Mark is supposed to face off against Chuck Liddell of the Ultimate Fighting League...
 * You know, in hindsight, it would've probably been easier for Alton to try to get the Chairman's job through Klingon Promotion.

Chairman Mark can kill you with his brain.
Or at least he has thought about it. Did you see the look he was giving Alton when Alton was mocking him for not getting brain freeze?

Kaga is a witch and Game Master a la Umineko no Naku Koro ni
And all of Iron Chef was a game between himself and other witches in what's known as the realm of gods to decide who was superior. Chairman Kaga was an image of himself to allow himself to play. The Iron Chefs were his "furniture" (a term used in Umineko for servants summoned by a witch).

In the end, the only challenge Kaga had was himself.
 * He is now playing a second game, using a different image-Chairman Mark-and different furniture-the American Iron Chefs. So far this game has no victor.
 * In a crossover with a Death Note WMG, Kaga could possibly have been an opponent to the witches Kira and Lawliet in the game that led to the events of Death Note (movie canon only). The most telling evidence to that is the fact that Soichiro Yagami greatly resembles Chairman Kaga. If he did, he technically won that game, due to having the last piece standing, but it would have been a Pyrrhic Victory.
 * One of the other (unnamed) witches uses Kandagawa as his image, and the Kandagawa and Ohta Factions as his furniture. The 21st Century battle was both a last grudge match between Kaga and the unnamed witch and a chance for Kaga to fine-tune his newest furniture-Bobby Flay.

Chairman Koji is a descendant of the Kaga family.
For those that don't watch Futurama, he was the Chairman-Expy in the Affectionate Parody of Iron Chef in "The 30% Iron Chef". And Futurama does take place a millenium in the future. Who's to say that he isn't a descendant of the Kaga family, somewhere?
 * Assuming Kaga and his descendants had an average of 2 children around age 30, after a millenium he would end up with about 2^33, or 8,589,934,592, descendants. That makes it incredibly likely.

Chairman Mark Wants to Return to Japan to Ultimately Usurp Chairman Kaga.
Chairman Mark's ambition is to return Iron Chef to Japan and reign there as true Chairman. The show may be over in Japan, but Kaga's legendary status as Chair of Chairs still stretches over Mark, who wants to reign under his own steam. He is slowly amassing his own army of Iron Chefs to return and challenge Kaga's chefs.

An epic clash in Kitchen Stadium will ensue. Morimoto will defect halfway through the battle and sabotage Team America's dishes. The Chairmen will have a Ham off which will end with Mark fracturing his hip. All will seem lost for Iron Chef America until...

Alton Brown is using the Next Iron Chef competition to get his own Iron Chef and take the show over after the Iron Chef War.
Going off the "Alton Brown is The Starscream" theories, Alton Brown initially proposed this competition under the impression that these new Iron Chefs would be wordlessly loyal to the Chairman. (Batali's fallout with Food Network stems from his realizing the horrible truth behind Kitchen Stadium. He will be victim of a tragic umami-related death soon.)

Alton realizes that Chairman Mark's ambition to usurp Kaga is foolish in its own right, but he sees a possibility in the NIC competition. Unbeknownst to Mark, Symon is already working for Alton; Morimoto will join him soon after. Along with the Next Iron Chef, Morimoto, and Symon, Alton Brown will hang back during the Iron Chef War until Sakai has exhausted himself and Team America is all but depleted. Morimoto will reveal his true allegiance to Alton Brown and, with a unprecedented display of grandiosity, will cast both Kaga and Mark down and reign as the true Chairman with Morimoto, Symon and the Next Iron Chef (who will be Mehta).
 * ...Pass the popcorn. (No, it will be Garces. Wanna shake on it?)
 * (Deal.)
 * (It is Garces.)

Bobby Flay is An Ice Person.
In the eggnog/ice sculpture battle, someone joked about Old Man Winter looking a lot like Flay. And well...that'd be cool, admit it.

Alton Brown wants to challenge an Iron Chef.
Maybe it's a part of one of the above WMGs, maybe not. But seeing how Alton did say, "so this is how it feels," and touted himself (exaggeratedly, but what do you expect?) as a force to be reckoned with. He wants to challenge an Iron Chef.

It's not like there isn't a precedent. Yukio Hattori had challenged two Iron Chefs before (and lost).

As for why Mark hasn't accepted Alton's challenge -- depending on how you view him, he either wants to spare Alton the possible agony of defeat or doesn't want to risk Alton winning and gaining more clout in Kitchen Stadium.

The substitute commentator should Alton challenge an Iron Chef would be one of three choices:
 * 1) Ted Allen. He knows as much about food as Alton, and he's experienced in commentating: He had been a floor reporter alongside Kevin Brauch in the Thanksgiving special.
 * 2) One or more of the Iron Chefs. Who better to talk about a battle than those that have done it before? Plus, there is a precedent: Iron Chef Ishinabe filled in for Hattori during his first battle. (Personally, if it's this, let's hope it's both Flay and Symon. The banter would be hilarious.)
 * 3) A former challenger. Probably one from Food Network's stable. Again, a precedent: long time Iron Chef rival Toshiro Kandagawa filled in for Hattori during his second battle.

[http://www.wherethehellwasi.com/categories/foodstuff-fluff/good_eats_amazing_feats.html In the first, as-yet-unaired episode of Iron Chef America, Alton Brown single-handedly defeated an all-star team of Bobby Flay, Cat Cora, and Hiroyuki Sakai. The secret ingredient was 'whimsy'.]

There is a war going on, but not between Kaga, Mark, and Alton.
It's between Mark and the Chairman from the Japan Cup.

The Chairman from the Japan Cup is also one of Kaga's nephews. He tried to carry on his uncle's legacy, but failed spectacularly. Meanwhile, Mark tried elsewhere, in America, where Iron Chef was still a popular show, and succeeded where the Chairman failed.

The Chairman, bent on revenge against Mark for stealing what he feels is rightfully his, is secretly training the six remaining Iron Chefs for a battle royale against Mark's Iron Chefs. Morimoto will be specifically targeted for 'turning traitor' and going to Mark's side.

Mark is aware of this; hence, he held the two Next Iron Chef competitions to build his numbers up so he can be evenly matched against the Chairman. Batali leaving threw Mark for a loop, but he has an ace in the hole: Alton Brown. All the supposed antagonism between them is to throw off the Chairman (who might be watching the show). Mark may name Alton an Iron Chef, either by giving Alton the same wager Kaga gave Hattori (defeat an Iron Chef and you can become one yourself), or by an impromptu "knighting" on the day of reckoning.

These would be the battle lines:
 * The Chairman, Sakai, Chen, Kobe, Ishinabe, Michiba, Nakamura
 * Mark, Alton, Morimoto, Cora, Symon, Flay,

Admittedly, once any of the older Iron Chefs dies, this immediately goes into the Jossed pile. But god, it was fun to imagine.

Mark is grooming Alton to be his successor.
Why would Alton try to usurp Chairman Mark when he's due to inherit Kitchen Stadium soon anyway?

For reasons currently unknown, Mark has decided to retire. Rather than close down Kitchen Stadium as his uncle had, he decided to name Alton Brown his successor. The hard time he gives Alton is because he's a believer of 'tough love', unsurprising given his martial arts background.

This is also why Alton had a big hand in The Next Iron Chef and filled the Chairman's role in the Super Chef battle: this way, he's not a complete novice when Mark finally hands the reins over.

Kaga is fluent in French.
Check the France special. When Kaga is talking to Pierre Gagnaire, and later to the Duc and Duchesse de Brissac, there is no translator in sight.

Now the question becomes, why is Kaga fluent in French? Dollars to donuts, he spent many years in France before going back to Japan to found his Kitchen Stadium.

The Chairman in Iron Chef UK is the black sheep of the family.
Proof: it was almost a decade before we learned he existed. Family is very important in Japan; he must have lost face. He has even lost the right to use his own name.

What might happen in the eventual Grand Finale of Iron Chef America
Because all good things eventually come to an end. One or more of these things might happen, if and when they close KSA down for good:
 * Alton finally challenges an Iron Chef
 * Kitchen Stadium America has their own King of Iron Chefs tournament.
 * If Cat Cora wins, She Is the King comes into play.
 * The winner challenges a famous chef.
 * The winner challenges Alton Brown
 * The winner takes on Sakai to fight for the 'God of Iron Chefs' title.
 * Stuff Blows Up.
 * It was all a dream.
 * Chairman Kaga makes one final appearance for this finale (admittedly unlikely to happen).
 * A Sopranos-esque ending.
 * One final Morimoto vs. Flay match, cause if you count the battles where they team up with someone or if you don't, they're still evenly matched, so one last grudge match.