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[[File:Yamiyugiwakingthedragons.jpg|thumb|Yami Yugi's first encounter with the Seal of Ochricalcos. ]]Later that night, a group of perpetrators broke into [[Kame Game]] and stole the God Cards. Yami Yugi meets up with them and Duels one, known as [[Gurimo]], who, during the Duel activates a [[field Spell Card|field Magic Card]] called "[[The Seal of Orichalcos (anime)|The Seal of Orichalcos]]", which entraps himself and Yami Yugi inside a magical force field. Gurimo explains that by using his new Magic Card, he and Yugi are cut off from the outside world and only he who wins the Duel can escape the full power of the "The Seal of Orichalcos", as it will extract only the male loser's soul to awaken [[the Great Leviathan]]. Gurimo Summons the stolen "[[Obelisk the Tormentor (anime)|Obelisk the Tormentor]]", who is affected by the "Seal". Yami Yugi manages to destroy "Obelisk" and defeat Gurimo, sealing Gurimo's soul, but does not recover the God cards.

Yami falls into depression and guilt over what he let happen to Yugi. As he continues his travels, he and Téa are split from Joey and Tristan on a train hijacked by Rex and Weevil. Weevil, seeking revenge for his loss in [[Duelist Kingdom]], Duels Yami on the roof, using "The Seal of Orichalcos". "Timaeus" refuses to assist Yami when he plays it because of his actions in the last Duel. When Weevil tricks Yami into thinking he's permanently lost Yugi's soul, Yami goes berserk and recklessly attacks him by using the combo "[[Breaker the Magical Warrior (anime)|Breaker the Magical Warrior]]" with "[[Berserker Soul (anime)|Berserker Soul]]", continuing even after Weevil's Life Points reach 0. Téa stops his constant and vengeful attacks, pointing out he's already won the Duel, but not in time for them to escape the out-of-control train, as after the Duel, it derails itself and falls off a cliff.

Afterwards, Yami and Téa meet up with the rest of their group and [[Seto Kaiba]], who had just escaped a harrowing rematch with a vengeful [[Alister]] atop his own jet. Kaiba takes them back to Domino City, which has become overrun with Orichalcos Soldiers. After Joey beats Valon, he loses his own soul in a Duel with [[Mai Valentine|Mai]]. On that note, Mai, who realized she made a mistake leaving Joey for "a madman who promised me power" (according to her), and who was filled with rage over losing Joey (as he was "the only one who ever cared about" her), challenges Rafael in a Duel to avenge Joey (believing that Joey would've done the same thing for her if their roles had been reversed), but also loses is defeated however she does not lose her souldue to the fact that "The Seal of Orichalcos" only takes male souls and not female souls.

Afterwards, Yami continued the Duel and activated the seemingly useless card that Pegasus created back at Industrial Illusions to battle Dartz and the Paradius Corporation—"[[Legend of Heart (anime)|Legend of Heart]]", which allowed Timaeus, [[Fang of Critias|Critias]], and [[Claw of Hermos|Hermos]] to assume their human forms as the [[Legendary Knight]]s. Sending them into battle against Dartz' "Orichalcos Shunoros" and later, his infinitely strong "[[Divine Serpent Geh]]", Yami was able to eke out his victory—but not before the Leviathan seemed to swallow Dartz whole. The Legendary Knights opened a tear in reality, returning the souls of the Chosen Duelists to their proper vesselsYugi's soul.

[[File:Yami Yugi (Ep183).png|left|thumb|200px|Yami with his the Egyptian Gods fighting against the Great Leviathan and Dartz.]]The final episodes of this arc brought Yugi, Joey, and Kaiba into battle with Dartz, who seemed to have merged with the Leviathan. Joined by every girl and woman from all over the inhabitants of the Dominion of the Beasts, they call forth their strongest monsters, as well as the Legendary Knightsworld, to battle the Great Beast. However, the Leviathan is too strong, despite their best effortsand they flee and hide in sadness, and absorbs the three Chosen Duelists while Yami gets absorbed into its own body. Yami convinced every boy and man from all over the people whose souls' dark feelings world imprisoned who fueled the Leviathan's power to remember every girl and woman from all over the good things in their livesworld who miss them terribly. In turn, the Chosen Duelists—as well as the Egyptian Gods, whose souls Dartz offered as a tribute to accelerate the Leviathan's awakening—were Yami was released, and Yami he left Yugi's body to join them in the battle. Through the power of the light of everyone's souls fueling every boy and man from all over the world inside the Leviathan had fueled the Gods, Yami was able to defeat the Leviathan, and Dartz was restored to his human form.