Noah displays the power of his virtual world by splitting up Yugi's gang and flinging them into the far reaches of his self-created universe! The first to duel under the all-new Deck Master System is Yugi against Big 1 Gansley's Deepsea Warrior! Can Yugi master the complex new rules, or will the rules master him?
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The final duel of Battle City begins. Yami Marik quickly turns it into a shadow game and sets it up so that if he or the Pharaoh loses, their host's soul will be destroyed. Yugi convinces the Pharaoh not to worry about him and to keep dueling to save Mai, Bakura and the good Marik. Yami Marik quickly discards his Winged Dragon of Ra to the graveyard, planning to revive it. Yugi manages to summon Slifer the Sky Dragon using his three Knights.
After defeating Joey and taking third place in the tournament, Kaiba plans to destroy the Duel Tower and bury his past forever. Ishizu and Mokuba convince him otherwise, and he gives Yugi one all-powerful card that could give him a chance to defeat Marik in the final duel.
Joey manages to gain one of Kaiba's strongest cards to help him advance in the duel. Meanwhile, Téa – possessed by the good half of Marik's soul – fights Yami Marik for control of the Millennium Rod.
Tired of Kaiba's constant ridicule, Joey challenges Kaiba for third place in the Battle City tournament.
Kaiba's final move forces the duelists to use only three cards, forcing to use the best cards in the decks to win the duel.
Kaiba gains a lead in the duel when he summons three Blue Eyes White Dragons. Yugi's hopes of winning come to an end, but receives some encouragement from Joey and stays strong in the game. Meanwhile, Joey's dreams and the ongoing duel cause Joey to awake.
With the destruction of both their monsters, Kaiba and Yugi are presented with a vision of the High Priest's legendary battle against the Pharaoh. Kaiba believes this to be a mere illusion, but Yugi knows that it is a vision of the past. The duel continues with Kaiba and Yugi attacking with their signature cards.
Kaiba is able to summon Obelisk the Tormentor, to the field, putting it at odds with Yugi's own Slifer the Sky Dragon.
Kaiba and Yugi compete to summon their monsters to the field, but each is hindered by the other's strategies.
The second duel of the semi-finals begins with Yugi dueling Kaiba for the second spot in the grand final and the chance to duel Marik. Kaiba draws Obelisk on his first turn, but Yugi thwarts his attempts to summon it with Lightforce Sword.
Despite surviving Marik's onslaught, Joey is weakened by the shadow game's effects and succumbs just as he is about to win the duel. Yugi struggles to find hope after losing his best friend to the Shadow Realm.
With life points dropping and his monsters unable to attack, Joey summons a monster that proves to be his saving grace, prompting Marik to unleash Ra.
Marik's duel tactics eat away at Joey's deck and his life points. Joey's comeback strategy, however is hindered by Marik's new monster on Joey's side of the field.
Marik brings Joey and himself to the Shadow Realm, where each duelist's heart is linked with his monsters, suffering the pain that the monsters feel.
With the conclusion of the four-way duel, the match-ups for the semi-finals are determined — Joey will duel Marik while Yugi will be facing off against Kaiba.
With Lector's Jinzo Deck Master destroying all of Kaiba's traps, Imperial Order destroying all his spell cards, and Lector's unreachable Satellite Cannon striking from space, Kaiba doesn't seem to stand a chance. Mokuba's unwavering faith in Kaiba keeps him believing that his brother will pull out with a victory, but Noah has plans to ruin their brotherhood.
As Nesbitt (in Tristan's body) kidnaps Mokuba, Kaiba is forced to duel Lector, the former assistant to his stepfather. For Lector, the duel is personal, as he plans to take what he believes is rightfully his—KaibaCorp. Meanwhile, Tristan rejoins the group his friends do not recognize him, since his mind has been downloaded into a mechanical monkey.
With Tristan gone and Serenity in shock, Duke attempts to defeat Nesbitt by himself. But when Orgoth the Relentless is destroyed by his Perfect Machine King, Duke tries to help Serenity regain confidence in her abilities. The two later remember Tristan's face down card, hoping it will help them win.
Tristan, Duke and Serenity duel Nesbitt, the Big 5's mechanical expert. Serenity's lack of experience with the game and Nesbit's powerful machine monsters create a tragic end for Tristan.
Joey attempts to pull through with several luck-based cards, but Johnson's cheating tactics ruin all his chances, until an angry Noah puts a stop to him.
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