| No.
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Original release date
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Original ISBN
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English release date
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English ISBN
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| 1 | March 4, 2005 | 4-08-873822-5 | October 6, 2009 | 978-1421530062 |
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- Duel R1: "A Wicked Shadow...!?" (邪悪なる影…！？, Jāku Naru Kage...!?) / "A Wicked Shadow!"
- Duel R2: "Avatar's Menace!!" (アバターの神威！！, Abatā no Shini!!)
- Duel R3: "KC Tournament, Start!! (ＫＣ決戦、開始！！, Kei Shī Kessen, Kaishi!!) / "KaibaCorp Duel Begins!!"
- Duel R4: "Menace of the Immortal Deck!!" (不死デッキの脅威！！, Fushi Dekki no Kyōi!!) / "Terror of the Immortal Deck!!"
- Duel R5: "Jonouchi's Clever Plan" (城之内の奇策, Jōnouchi no Kisaku) / "Jonouchi's Plan"
- Duel R6: "Threat of the Armored Unit!!" (威の機甲部隊！！, I no Kikōbutai!!) / "Marvelous Armed Division!!"
- Duel R7: "Jonouchi, Again!!" (城之内、再び！！, Jōnouchi, Futatabi!!) / "There Goes Jonouchi"
- Duel R8: "Dweller in the Deep Darkness!!" (深き闇の住人！！, Fukaki Yami no Jūnin!!) / "Dweller in the Dark!!"
- Duel R9: "A Fearsome God, Descends!!" (恐怖の神、降臨す！！, Kyōfu no Kami, Kōrin su!!) / "A Fearsome God Descends!!"
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| Set after Battle City, Yako Tenma hacks Kaiba Corp. and takes it over while Seto Kaiba is away. He then challenges Dark Yugi to a duel and overwhelms him with The Wicked Avatar, a creature on par with the Egyptian God Cards. Yako abruptly cancels the duel and kidnaps Anzu, revealing he blames Yugi for Pegasus' death. He tells the boys to fight their way up Kaiba Corp. past his card professors to rescue Anzu. The first professor, Deschutes Lew, reveals Anzu's soul has been sealed in a card and gives it to them. Dark Yugi defeats his defensive deck. He then defeats Tilla Mook's Vampire deck and Jonouchi borrows her duel disk since he forgot his. Jonouchi and Honda fall down a trap door into the basement where Jonouchi defeats Klamath Osler's Antlion deck. Dark Yugi defeats Kirk Dixon's Machina deck. Jonouchi defeats Pete Coppermine's Mutant deck. Dark Yugi defeats Maico Kato's Forest deck. Dark Yugi meets Yako halfway up the building and duels him, only to be shocked when he summons another Wicked God, The Wicked Dreadroot. |
| 2 | December 2, 2005 | 4-08-873893-4 | December 1, 2009 | 978-1-4215-3007-9 |
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- Duel R10: "A World Ruled by Terror!!" (恐怖が支配する世界！！, Kyōfu ga Shihai suru Sekai!!)
- Duel R11: "The Conclusion, And...!?" (決着、そして…！？, Ketchaku, Soshite...!?) / "The Showdown, And Then...?!"
- Duel R12: "Jonouchi, Cornered!?" (城之内、絶体絶命！？, Jōnouchi, Zettaizetsumei!?) / "Curtains for Jonouchi?!"
- Duel R13: "Enter, Seto Kaiba!!" (海馬瀬人、登場！！, Kaiba Seto, Tōjō!!) / "Enter Seto Kaiba!!"
- Duel R14: "The Menace of "Mist"!!" ("ミスト"の脅威！！, "Misuto" no Kyōi!!)
- Duel R15: "Ultimate Life Form, Descend!" (究極の生命体、降臨！, Kyūkyoku no Seimei-tai, Kōrin!) / "Advent of the Ultimate Life-Form!!"
- Duel R16: "The Tenma Brothers' Secret...!!" (天馬兄弟の秘密…！！, Tenma Kyōdai no Himitsu...!!)
- Duel R17: "The Elf Warriors!!" (エルフの戦士たち！！, Erufu no Senshi-tachi!!)
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| After a hard fought duel, Dark Yugi defeats The Wicked Dreadroot, but Croquet cancels the duel and reveals that his opponent was Yako's twin brother Gekko under mind control. Now snapped out of it, they explain that Yako plans to use Anzu's soulless body as a vessel to resurrect Pegasus. Gekko also explains that Yugi can put Anzu's card on his duel disk to communicate with her, briefly reuniting them. Jonouchi defeats Mendo Cino's Mantis deck. Seto and Mokuba Kaiba arrive to take Kaiba Corp. back. Seto defeats Willa Mette's White-Horned Dragon deck and enters the building. Yugi and Gekko meet a resurrected Bandit Keith, then since Dark Yugi is exhausted, Gekko faces Ted Banias's Beast deck with his Elf deck after putting away his deck with The Wicked Dreadroot. |
| 3 | September 4, 2006 | 4-08-874260-5 | February 2, 2010 | 978-1-4215-3008-6 |
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- Duel R18: "The Perfect Duel!!" (パーフェクト決闘！！, Pāfekuto Kettō!!)
- Duel R19: "Helpless Jonouchi!!" (翻弄される城之内！！, Honrōsareru Jōnouchi!!) / "Jonouchi...Helpless?!"
- Duel R20: "The Anger of Seto Kaiba!" (怒りの海馬瀬人！, Ikari no Kaiba Seto!) / "The Rage of Kaiba!!"
- Duel R21: "The Truth of the R.A. Project!!" (Ｒ・Ａ計画の真相！！, Āru Ei Keikaku no Shinsō!!)
- Duel R22: "Showdown in Outer Space!!" (宇宙空間の決戦！！, Uchū Kūkan no Kessen!!) / "Outer Space Showdown"
- Duel R23: "Toy Magic!!" (トイ・マジック！！, Toi Majikku!!)
- Duel R24: "Another Partner!!" (もう一人の相棒！！, Mō Hitori no Aibō!!)
- Special Duel: "Dark Ruler, Summoned!!" (冥王、召喚！！, Mei-Ō, Shōkan!!) / "Summon The Dark Ruler!!"
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| Gekko defeats Ted. Bandit Keith beats Ted up, then offers to lead Yugi and Gekko to Yako. Jonouchi defeats the shy Reiko Kitamori's Puppet Chess/deck destruction deck while Seto reaches Yako, who explains his plan. Since Dark Yugi is still tired, Yugi takes over and defeats Depre Scott's Cosmic Deck with his Toy deck.
In a special chapter set before or after the story, the bully Masumi Momono duels people by using decks specialized to counter them, then takes their cards after he wins. Despite using a Light deck to counter Dark Yugi's Dark monsters, Dark Yugi defeats him. |
| 4 | April 4, 2007 | 4-08-874351-2 | April 6, 2010 | 978-1-4215-3009-3 |
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- Duel R25: "Richie's Fight, Start!!" (リッチー戦、開始！！, Ritchī-sen, Kaishi!!) / "Gekko vs. Richie"
- Duel R26: "Pegasus' Minion!!" (ペガサスミニオン！！, Pegasasu Minion!!) / "Pegasus's Prodigies!!"
- Duel R27: "Respective Battle!!" (それそれの闘い！！, Soresore no Tatakai!!) / "To Each His Own Battle!!"
- Duel R28: "Apex Arena!!" (頂点の闘技場！！, Chōten no Tōgi-ba!!)
- Duel R29: "Summon The Evil God!!" (邪神召還！！, Jashin Shōkan!!)
- Duel R30: "Unsurpassable "1"" (超えられない「１」, Koe Rare Nai "Ichi") / "The Invincible "1""
- Duel R31: "R.A. Launched!!" (Ｒ・Ａ発動, Āru Ei Hatsudō) / "Rebirth of Avatar!!"
- Duel R32: "Pegasus Summoned!?" (ペガサスの召喚！？, Pegasasu no Shōkan!?) / "The Resurrection of Pegasus?!"
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| Gekko then faces Richie Merced's Cowboy deck, but unfortunately loses, so Richie locks the door and refuses to let him and Yugi advance. Bandit Keith then challenges Richie for his rare black duel disk. Jonouchi and Honda beat up guards until they meet Mokuba who shows them a path. After Yako explains Pegasus created the Wicked God Cards to counter the Egyptian God Cards, Seto duels Yako but loses when Yako summons both The Wicked Avatar and The Wicked Dreadroot. Keith defeats Richie with The Wicked Eraser and claims his black duel disk. Yako says his project is almost complete and Pegasus is almost reborn. Yugi and Gekko find an alternate path and hurry to Yako and Anzu's body. Mokuba hacks the system and prevents the resurrection, infuriating Yako. After Dark Yugi defeats Cedar Mill offscreen, they meet Jonouchi and Honda, but Keith challenges Jonouchi, seeking revenge for his previous defeat, so Jonouchi tells the others to go ahead. |
| 5 | April 4, 2008 | 4-08-874441-1 | June 1, 2010 | 978-1-4215-3010-9 |
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- Duel R33: "Rematch!! Keith vs. Jonouchi" (再闘!!キースVS城之内, Saito!! Kīsu Tai Jōnouchi)
- Duel R34: "Last Evil God, Descend!!" (最後の邪神、降臨！！, Saigo no Jashin, Kōrin!!) / "The Last Jashin Rises!!"
- Duel R35: "Jonouchi, Fight Back!!" (城之内、反撃！！, Jōnouchi, Hangeki!!) / "Jonouchi Strikes Back!!"
- Duel R36: "Devil God Destroyed! (邪神消滅！, Jashin Shōmetsu!) / "Death of a God!!"
- Duel R37: "Final Showdown!" (最終決戦！, Saishū Kessen!) / The Final Showdown
- Duel R38: "Offense and Defense of the Summoned God" (神召喚の攻防, Kami Shōkan no Kōbō) / "Clash of the Gods!!"
- Duel R39: "Godspeed Summons!!" (神速召喚！！, Shinsoku Shōkan!!) / "Speed Summon!!"
- Duel R40: "Ruler of the Field" (世界の支配者, Sekai no Shihaisha) / "Reign of the Avatar"
- Duel R41: "Existence of Another Person" (もう一人の存在, Mō Hitori no Sonzai) / "The Other"
- Duel R42: "Clash! God vs. Devil God" (激突！神ＶＳ邪神, Gekitotsu! Kami Tai Jashin) / "God vs. Evil God!!"
- Duel R43: "Annihilation!! And..." (対消滅！！ そして…, Tsuishōmetsu!! Soshite...) / "Mutually Assured Destruction"
- Duel R44: "The End of the Battle" (闘いの果て, Tatakai no Hate)
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| Despite Bandit Keith trying to cheat, Jonouchi defeats his Motor deck and The Wicked Eraser, claiming the black duel disk. Dark Yugi finally faces Yako. When he summons The Wicked Avatar, its malevolent power absorbs Anzu's soul and restarts the resurrection project. Dark Yugi destroys The Wicked Avatar, restoring Anzu's soul to her body and freeing Yako from its influence, letting him see a vision of Pegasus. Apologetic, Yako attempts to surrender, but Gekko convinces him to continue the duel just for fun. Dark Yugi ultimately wins. Yako apologizes and rips The Wicked Avatar in half. Everyone is reunited with Anzu. The card professors also apologize and Jonouchi gives Tilla Mook the black duel disk. |
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