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Yet another spinoff of the Yu-Gi-Oh! series, Yu-Gi-Oh R is written by Akira Ito, one of Kazuki Takahashi's assistants on the original manga. The story, taking place between the Battle City and Memory World arcs, kicks off with Yako Tenma, Pegasus' adopted son and protege, taking over Kaiba Corp and challenging Yugi to a duel. There, he reveals "The Wicked Avatar," one of three "Evil Gods" that Pegasus had designed before his death. After destroying Yugi's Osiris in one blow, Yako kidnaps Anzu and takes her to the Kaiba Corp building, where he intends to "sacrifice" her in "Project RA" as revenge for Yugi causing Pegasus' death at the end of Duelist Kingdom.

Yugi, Jounouchi, and Honda race to Kaiba Corp to rescue Anzu, only to find that Yako has commissioned the Card Professors--thirteen professional American duelists--to block their way. Our heroes must battle their way up the tower to stop Yako before he can carry out his plans. Meanwhile, Kaiba and Mokuba, not exactly thrilled with Kaiba Corp getting taken over again, storm the castle, er, skyscraper, to reclaim the company.

Notable for its speedy pacing in comparison to the earlier series; duels usually only take up one or two chapters instead of dragging on and on. Oh, and throughout the whole series, nobody even tries to kidnap Mokuba.

All five volumes have been released in the U.S. under Viz's Shonen Jump label.

Tropes used in Yu-Gi-Oh! R include:
  • Aerith and Bob: The Card Professors' names range from perfectly normal (Kirk Dixon, Pete Coppermine, Ted Banias) to downright strange (Deschutes Lew, Klamath Osler, Willa Mette). See Theme Naming below.
  • All Your Base Are Belong to Us: Let's face it, Kaiba Corp is pretty much the Mokuba of the Fiction 500.
  • Avenging the Villain: Unfortunately, Yako's trying to get revenge on the wrong person; other than defeating him at the end of Duelist Kingdom, Yugi didn't have a thing to do with Pegasus' death. The real culprit never even makes an appearance.
  • Badass Grandma: Mrs. Maico Kato, a tea-drinking, wheelchair-bound, doting grandmother... who also happens to be a highly-ranked professional Duelist.
  • Batman Can Breathe in Space: Depres Scott's Theme Deck plays with this; monsters in space are assigned a number of "life stars" based on their level and lose one at the end of each turn. Once they run out, they're automatically destroyed.
  • Big Creepy-Crawlies: The Theme Deck of Mendo Cino, one of the Card Professors, consists of mantises. The Dreadscythe Harvester is larger than even the duelist who uses it.
  • Big No: Yuugi lets one out when he believes that he's failed to save Anzu in time.
  • Blank White Eyes: A Running Gag in this series involves this happening to Jounouchi when he's overwhelmed with indignation. Don't worry; it's Played for Laughs.
  • Brainwashed and Crazy: Yako is possessed by the Wicked Avatar. Gekko could also qualify during the period he is controlled by Yako.
  • Brick Joke: After Yugi defeats Tilla in the first volume, Jounouchi asks if he can borrow her Duel Disk, since he hadn't brought his with him. At the very end of the series, he's seen repaying the favor by giving her the special black Duel Disk.
  • Cain and Abel: Inverted - Yako is the younger but evil brother, while Gekko is the older but good brother.
  • Catchphrase Interruptus: Okay, not really a catchphrase, but Jounouchi's attempt at making a badass speech after beating Mendo gets drowned out by the roar of Kaiba's jet engines.
  • Calling Your Attacks: Like he did with Marik in the main series, Jonouchi parodies this - when Jonouchi summons Fiendish Engine Omega, after stealing it from Bandit Keith's hand, he names it's attack "Jonouchi Crusher!". Lampshaded by the comic itself, as it adds the helpful note "Name coined by Jonouchi" underneath.
  • Cheaters Never Prosper: Bandit Keith tries to sneak a Ring Of Destruction card into his hand from outside his deck during his duel against Jounouchi. Of course it doesn't work.
    • Chekhov's Gun: The anti-cheating feature of the Duel Disks had never been triggered before in the story- it was only mentioned as part of the summary of the special rules of the series at the end of the previous volume.
  • Cherry Tapping: The Wicked Avatar is always exactly ONE attack point stronger then the strongest monster on the field, but as Yakou points out, that one attack point makes all the difference.
  • Cloning Blues: Played with, as while Yakou and Gekko are natural identical twins, flashbacks reveal that Yakou always felt like an inferior copy of his twin brother.
  • Continuity Nod: At least in the Viz translation, Kaiba claims that the caliber of duelists at his company's latest sponsored tournament isn't quite to par and that perhaps he should think about opening up a school
  • Curb Stomp Battle: Near the end of Volume Four, Yami crushes a Card Professor in a single panel with Osiris.
  • Distressed Damsel: Anzu. Mokuba actually gets left alone for once.
  • Double Entendre: One of Mendo's cards forces each player to pay 1000 Life Points to normal summon any monsters. It's called "Labor Pain."
  • Dungeon Bypass: Partial example; Kaiba handily defeats one of the Card Professors, who prepares to hand over the key card needed to get into the building... only for Mokuba to cheerfully announce that he's finished hacking through Yako's changes to the security system. Kaiba's sole reason for bothering with the duel in the first place was that he wanted a "warmup".
  • Eagle Land: Not only are the Card Professors Americans, but guess who's back...
  • Evil Counterparts: The Wicked Gods for the God Cards.
  • Evil Laugh: Depres indulges in this when he has Yugi against the ropes. Even Richie thinks he sounds over the top.
  • Expy: Yako could qualify as Pegasus' Expy. Goes crazy after losing a loved one? Check. Wants to bring said loved one back regardless of what it takes? Check. Takes someone close to Yugi as hostage? Check. Even lampshaded by Gekko when he mentions Yako is just like Pegasus.
  • Eye Scream: That eye-melting scene...
  • Grand Theft Me: Project RA's goal is to remove Anzu's soul from her body and put Pegasus' soul in her place.
  • Heroic BSOD: Yami has one after seeing what's become of Anzu's soul on top of how tired he was, and Kaiba has one after being defeated by Yako (or so Yako thought).
    • Kaiba had one too, after losing a duel.
  • Hoist by His Own Petard: A very mild and non-violent example of this happened to Kirk Dixon, who, after losing his duel to Yugi, became so distraught by his loss he stumbled upon a booby trap he had set up himself and was promptly sent downstairs into the basement.
  • Hope Spot: During Gekko's duel with Richie, just as Gekko is about to win with a devastating direct attack, there is a sudden flash of light and Richie has won. A quick flashback next chapter reveals what happened, and leads into a nasty Tearjerker.
  • I Have Your Non-Girlfriend: Yako kidnapping Anzu drives the entire plot
  • It's All Upstairs From Here: Of course Yako's going to wait for Yugi on the top floor of the Kaiba Corp building. Jou and Honda have it even worse, since they fell through a Trap Door early on and ended up in the basement. Subverted with Kaiba and Mokuba, who came in through the roof.
  • Jerkass: Not like this is any sort of surprise, but Bandit Keith pretty much started this whole mess by telling Yako that Yugi killed Pegasus. Of course, this is all untrue, but Keith couldn't care less either way, as long as he gets the chance to duel Jounouchi again.
  • Kick the Son of a Bitch: Bandit Keith gets to literally be both on the giving and the receiving end of this one. The former is when he suddenly starts beating Ted Banias up and increases the amount of debt he owes him, all for losing a duel against Gekko. The latter comes almost immediately afterwards, when Richie starts to kick Keith around for not following orders once they meet up.
  • Law of Chromatic Superiority: The black Duel Disk used by the highest-ranked member of the Card Professors guild. Gekko even compares it to a black belt in martial arts.
  • Mad Eye: So what was your first clue that Yako wasn't playing with a full deck?
  • Meaningful Name: Humorous, unintentional example: one of the Card Professors is named Tilla Mook.
  • Mission Control: Mokuba takes on this role, deactivating Yako's security measures, monitoring the Duel Server's status, and keeping the others filled in on the current situation.
  • Mood Whiplash: Chapter 27 opens with Jounouchi and Honda beating up tons of Mooks, with a humorous Lampshade Hanging by Jounouchi about how long its been since he fought someone with his fists instead of cards. Then we shift back to Yuugi and Gekko, who has just lost and thus prevented Yuugi from being able to advance and rescue Anzu. Ouch.
  • Near Villain Victory: Yakou has just defeated Seto Kaiba, Bandit Keith successfully summoned The Wicked Eraser, and now Anzu's soul is being consumed to revive Pegasus...wait, why is it stopping? Well, thanks to Keith's Revenge duel against Richie just a moment ago, the Kaiba brothers were able to force the program to stop!
  • Necromantic: Yako.
  • Nightmare Fetishist: Tilla, who refers to her Vampire's Curse card as her "master" and allows it to suck her blood to grow stronger. (That's right - the holographic vampire actually bites her. You can see the bite marks in her neck if you look closely.)
  • No Fair Cheating: The duel disks sound an alarm if you try to make an illegal move.
  • Not So Different: Lampshaded by Richie after Yuugi defeats Depre, noting that Yuugi's desire to save Anzu is very much the same as their desire to revive Pegasus.
  • Not So Stoic: Depres Scott. Normally he shows little emotion, but during his duel with Yugi he lets loose with an Evil Laugh when he has Yugi near defeat, and then breaks down in tears (after losing to Yugi) so much Richie has to get someone to take care of him.
  • People Jars: Subverted. Not only are all the Duel Monster "specimens" simply holograms, but the one human among them put himself in there so he could prank anyone who came by.
  • Phantom Zone Picture: Anzu's soul gets placed in a playing card the same way Pegasus used to imprison his victims. Yugi can actually communicate with her by placing the card in his Duel Disk.
  • Punch Clock Villain: Most of the Card Professors don't have anything personal against Yugi or his friends--they're just in it for the pay, and they don't even try to cheat. Then again, they don't seem to have any problem with the idea of an innocent girl getting sacrificed, either...
  • Revenge by Proxy: Yako targets Yugi by turning Anzu into a Human Sacrifice so he can resurrect Pegasus.
  • Schrodingers Cat: Bandit Keith looks remarkably healthy for somebody who was Mind Raped to death during the Duelist Kingdom finals...
    • Mind you, it is revealed that Bandit Keith is alive because he was the test subject for the R.A. Project, which is the source of Yako's confidence that his ambitions will be successful.
  • Sempai-Kohai: Yako is Pegasus' kohai.
  • Shapeshifter Guilt Trip: During the final showdown against Yako, The Wicked Avatar takes Yugi's form. Yako says it's a manifestation of Yugi's hatred for his other self for being the true Game King and preventing Yugi from earning that glory himself. Yami almost falls for it, until Yugi briefly takes over and insists that he would never have been able to make so many new friends or broaden his horizons if it hadn't been for his other self.
  • Shrinking Violet: Reiko, whose first instinct upon encountering another Duelist is to run away, and is described as having no fighting spirit when she does duel. Ironically, she would have beaten Jounouchi if she had stuck to her passive deck destruction strategy instead of gaining the confidence to straight-out attack him.
    • Her whole approach to dueling was passive-aggressive, really, and was effective since her deck was so broken. Jou even lampshades this. See Underestimating Badassery for more.
  • Sixth Ranger: Gekko.
  • Spanner in the Works: Keith, when you consider that Yakko would've succeeded if Keith hadn't decided to get revenge on Richie
    • At the same time, Keith's duel with Richie was actually necessary for Yako to summon Pegasus' soul, since he needed the energy generated from summoning the Wicked Eraser. The REAL spanner was Seto and Mokuba Kaiba - Yako hadn't realised that Mokuba was in a place where he could do any significant damage, nor did he think that Mokuba could have used Keith's duel to shut down his program.
  • Symbol Swearing: Bandit Keith, lovable evil foreigner that he is, gets his speech liberally peppered with this in the Viz translation.
  • Tear Jerker: Seeing Yuugi in despair, watching Anzu's soul fade away as they reach out to each other, is not easy on the heart.
  • The Only One Allowed to Defeat You: Kaiba says this to Yugi almost word for word when they meet up.
  • Theme Deck: Naturally.
  • Theme Naming: The Card Professors are all named after Intel project code names, which are in turn named after the places where Intel labs are located, according to The Other Wiki.
  • There Is No Kill Like Overkill: Played with in Seto's duel with Yakou, as while Seto's gratuitous summoning of the Blue-Eyes Ultimate Dragon is ultimately his downfall, Yakou's similarly gratuitous summoning of two Evil Gods works just fine for him.
  • The Three Faces of Eve: Reiko Kitamori, Tilla Mook, and Mrs. Maico Kato
  • Twin Switch: Sort of - Yako pulls a Grand Theft Me on his twin brother, Gekko, in order to test his new deck against Yugi.
  • Underestimating Badassery: When Jounouchi first encounters Reiko Kitamori, he thinks she doesn't look too tough. And indeed, while Reiko is easily intimidated, She is in fact one of the most powerful duelists in the series, using a deck-destruction strategy that would put Seto Kaiba and Isis Ishtar to shame. Oh, and she only started playing Duel Monsters a month ago.
    • To be fair, Reiko was playing a Game Breaker of a mill deck. Not only in that one of her key cards, Battlefield Tragedy, is a Continuous Spell Card that forces the opponent to mill 5 cards every time they attack, making it 5 times more potent than the similar real-life card Gravekeeper's Servant, but she uses two copies at the same time for a total of 10 cards every time the opponent attacks, and even worse, combines it with cards that force the opponent's monsters into attacking each other, clearing the opponent's monsters and their deck to boot. Leave it up to the manga to come up with broken cards that can be counted on to be nerfed if they make it into the actual game. On the flipside, it is possible that Jounouchi could have won without having to goad her into attacking, had he the chance to attack on his own with the cards he had on field during the last turn, since a duelist loses only if they have to draw when their deck is empty.
  • The Unfavourite: Yako believed he was the worse duelist out of the two. Pegasus described Gekko as a perfect duelist, while Yako was "an unfinished rough diamond." Subverted by the end of the series, where it is revealed that Pegasus saw the potential in Yako to be a great duelist, hence the "rough diamond" metaphor, while Gekko had "perfected" himself and was incapable of growing any stronger.
  • Villainous Breakdown: Bandit Keith in the final volume, during his duel with Jounouchi.
  • Weak but Skilled: Gekko Tenma, who uses hordes of low attack monsters with potent effects, supplemented with spells and traps.
    • Yugi's Toy-themed deck is like this as well.
  • With Great Power Comes Great Insanity: Yako used to be a quiet, withdrawn young man. That all changed once he started creating the Evil Gods, which warped his grief over Pegasus' death into homicidal rage toward Yugi.
  • White Gloves: Yako wears them.