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Ark
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Okay, this bugs me, as a lot of people who ask me questions think Konami is in charge of the comic book, TV show, and card game. So I'm going to try and give a brief rundown of who's who.
At the top of the pyramid is Studio Dice, the personal company of Kazuki Takahashi, that is responsible for the creation of the Yu-Gi-Oh! IP.
Kazuki-sensei is the creator of Yu-Gi-Oh!, writing the original comic book and providing support for the TV shows with rough drafts, plot premises and ideas.

These days, he's fairly rich and Studio Dice is basically empty of staff.

Indications are he has a high level veto.
But for obvious reasons, he doesn't get involved that heavily in a media mix franchise of this size, and leaves well enough alone.

But supposedly Yu-Gi-Oh!'s lack of cash prizes and anti-Set Rotation attitude are demands set by him.
Next in the ladder is Kabushiki Gaisha Shūeisha, i.e. Shueisha Publishing Co., Ltd. They're the publishers of Yu-Gi-Oh!'s various comic books and Yu-Gi-Oh! news, via magazines such as Weekly Shonen Jump, V Jump and Saikyo Jump.
Think of it as the relationship between J.K. Rowling and Bloomsbury Publishing.

Shueisha is basically the biggest comic book publisher in Japan, who can basically turn things to gold, with multiple big titles under their belt. Maybe you've heard of a little thing like One Piece.
However, Shueisha's strength is pretty much a publisher, they rely on outside help and partners to expand their comic books into games, TV shows, etc.

That's where Nihon Ad Systems Inc. (NAS) steps in. Their job is adapting works to TV, managing IP/Copyright rights and...
international distribution. A vast number of decisions for managing the series ends up in their lap, and supposedly the artwork on cards is THEIR property, if the whole YGOPro/Dueling Network mess holds true.
ADK Holdings Inc. is the mother company for NAS, and is basically the third largest advertising agency in Japan.

Since 2018 it's been owned by Bain Capital, but in so far as we know, this is incidental.
Originally, NAS contracted Toei to make a TV show based on the Yu-Gi-Oh! anime, and contracted Bandai to make a card game based off of the comic and TV show.

Both of these went poorly. Toei's anime had lousy animation at cost of high profile music, actors, et al.
Bandai similarly made a poor, confusing, vaguely explained game with few if any terribly clear rules. Understandably, it didn't last long.

And Toei's attempt to revive their take on the IP with a movie kind of blew out.
"But Ark, where's Konami?! They run this series!"

No, they don't. Konami's rights for the game begin and end to create a CCG and related media, such as video games. That's where their duties begin and end mostly. The reason you hear about them the most is they're visible...
but the rest of the hydra tends to loom in the background. The whole "90% of an Iceberg is actually underwater" shtick is at play here.

You think Konami is charge because they're the ones that do the most active PR (the head most visible above water so to speak)
As to who is behind the anime series, those would be the various production committees. It's probably a pain to dig up who exactly is behind each of those, but it wouldn't be unlikely to assume NAS, Konami and Shueisha have seats at the table.
"But Ark, Konami you said isn't in charge", yes but they're a sponsor, sponsoring their toy, the game they licensed. It's an interconnected web.
NAS and the Production Committees for the YGO animes ultimately keep hiring Studio Gallop, a smaller firm, after the initial screw up by Toei.

Besides, YGO, noteworthy stuff I'll note include Transformers: Robots in Disguise, Eyehshield 21, and Bakuretsu Bar Hunter
The 2001 Robots in Disguise
As to the anime itself, that's a whole other hydra on its own terms, that I suggest looking up sources like Sakuga Blog who do plenty to explain the anime industry's sausage making.

But this is a good rough guide.
Notice how high up Script/Scenario Writer, Director and Producer are? That's why I tend to bring them up so much because they're essentially the beating heart of the TV show's engine
Also of note is TV Tokyo, a major partner in this that often broadcasts anime (Boruto's Dad and Bleach comes to mind) and has a fairly steady relationship with Toyetic IPs and Shueisha's various heavy hitters.
This leads to international licensing. Back in the early 2000s, NAS, TV Tokyo and Konami hammered out a deal with TV Producer and comic book artist Roger Slifer (as well as others), who was with 4Kids Entertainment at the time, to license Yu-Gi-Oh!
This was due to 4Kids' success with the Pokemon property, managing to get its foot in the door to the west.

As an aside:
…fancryinginthewilderness.blogspot.com/2012/02/meet-r…

Slifer himself found the whole censoring for the IP kinda silly, but acknowledges that that's what you have to do.
Any further licensing of the TV show around the world basically went through 4Kids, as per their deal with the original license holders, and more or less holds to this day.
4Kids I'll have to segue into here for a bit.

After 2008 or so, their fortunes basically shifted extremely poorly after getting a big sexy loan/rainy day fund from Lehman brothers... that turned into dust in the wind, when Lehman Brothers collapsed.
4Kids kept trying to pursue the next hot thing in kid's entertainment, but. By then basically everyone had already licensed/ran their own work.

Anime companies were beginning to import more and more of their own IPs.

Nintendo and the like had wrestled back control of Pokemon.
And most of the anime Shueisha kept providing 4Kids had this problem:

They were 'extremely violent' for Kids TV, by US Standards. Yes they were for elementary school and middle school children by Japanese standards but the US children's show media tends to be a 'ghetto'.
So with a string of clunkers due to enormous censorship, less than smart executive decisions, and trying to bank on really fringe IPs as the 'next big thing', 4Kids ended falling apart, but not before miring Yu-Gi-Oh! into a legal battle.
animenewsnetwork.com/news/2012-03-0…
You can go research it but essentially, the YGO IP holders tried to reclaim YGO like Nintendo and TPCi reclaimed Pokemon.

4Kids fought tooth and nail and settled based on technicalities, leaving a dub featuring Johnny Yong Bosch as Yuma in limbo forever.
However, the lawsuit combined with the company's collapsing financial situation basically killed them and led to them having to go to auction.

Which led to Saban and Konami having to fight things out.
Konami bought essentially the production studio arm of 4Kids and renamed it 4KMedia, but on the condition it had to air content on Saban's TV show blocks, which has left YGO languishing, dub wise, on NickToons in the US.
4KMedia has recently been retitled Konami Cross Media, meant to help serve as a licensing arm for multimedia for YGO and Konami's own in house properties (starting with Bomber-Man, Contra, Frogger)
Moving onto other international partners:

Formerly, UpperDeck Entertainment handled the localization portion of Yu-Gi-Oh!

This ended when the President hatched a hilariously comical scheme straight out of a bad Hollywood heist film.
yugipedia.com/wiki/Konami_v.…
I'll let the Yugipedia wiki talk about this more in depth, but suffice it to say UDE is no longer involved and the situation permanently ruined the company's reputation.
Let's see, I think there's one last major player to bring up currently, I believe.

Viz. They're a company owned in joint by Shogakukan and Shueisha. (Started as Shogakukan's arm but then Shueisha got an interest).

They own the rights to localizing the comics.
Any questions?
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