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The Pharaoh's Signature
Inside of his temple, Dartz announces to Rafael that he's lost the Pharaoh's signature; he can't trace the Pharaoh's movements from afar anymore. Rafael suggests he could be dead. Dartz is unsure, for once, but he is sure that something or someone is blocking his signature. Rafael offers to investigate.
Yami and Téa wake up in a hut somewhere and are greeted by a wolf-like dog and a small girl who introduces herself as Chris.
Both walk outside to find an elderly man named Ironheart picking up Yami Yugi's scattered cards. He notices the "The Eye of Timaeus" and seems to recognize it.
Ironheart: "You seem to possess an intriguing Card."
Yami Yugi: "It's a Card which I cannot use anymore..."
Téa inquires if they found Weevil's body. Ironheart announces that he entrusted him to some persons he knew and was taken to the nearest hospital (In the dub, Ironheart states he found nobody else besides Téa and Yami Yugi in the wrecked train). He comments that he was like a corpse, missing his soul. Both Yami Yugi and Téa confirm it. Ironheart then asks Yami what he plans on doing. Yami Yugi admits that he's searching for the soul of his partner.
Yami Yugi: "I'm not sure... I'd like, at the very least, to apologize to him..."
Ironheart then offers to guide them to a special place.
In the meanwhile, Rafael has found the remains of the derailed train half-sunk into a river. He deduces Yami Yugi is not within the remains, so he wonders where he has gone off to.
The Wastelands of Stone
After a long trek, they reach a valley where some structures and circles have been drawn: it obviously is a site of reverence for something. Ironheart explains that dead ones linger in here. They are beings which have a will of iron who cannot return. Their hatred is gathered here.
Lastly, within the center of the arena, some spheres of energy gather and give way to a spirit-like Yugi.
Yami Yugi goes apologize to him, but Yugi is upset about Yami Yugi's actions. Yami Yugi tries to explain to him that he's confused: he's not sure of what's good and what's bad. Yugi claims that he will prove if Yami Yugi is still stained by the 'darkness' of his heart. He admits that Yami Yugi is always the strongest when it comes to Duels, but Yugi says that he'll test him: if he cannot win, then he'll vanish.
Chris and Ironheart look on along with Téa. Ironheart mutters about having heard of the Nameless Pharaoh, and wonders if he'll be able to win. The very reason is that his first step is face his inner fears and conquer the darkness that dwells within his hearts; but, if he loses, the Pharaoh's spirit will remain here forever.
Since both Yugi and the Yami Yugi had identical hands and Decks, the duel would not be easy for a confused Yami Yugi to accept. On the other hand, Yugi had replaced his entire hand with a new one. Yami Yugi asks Yugi why he is behaving this way. Yugi responds in anger that he is just a reflection of him, that they are both exactly the same, so the darkness that is inside Yami Yugi's heart is also inside Yugi's heart. Knowing that what he said is untrue, Yami Yugi thought Yugi would take it back. However, Yugi says that is too late for him now, because Yami Yugi already showed him who he really is, an evil Pharaoh who only cares about himself; that he doesn't care what happens to others as long as he has power, and now it's Yugi's turn to return the favor. Yami Yugi is unaware, but recognizes the card Yugi drew from his deck and tells him to wait. Yugi, knowing that Yami Yugi knew what he drew, tauntingly announces that this is just the beginning. Yugi claims that this duel is the chance for Yami Yugi to look at himself from the inside, and there is only one card in his Deck that will make that happen, The Seal of Orichalcos. Yami Yugi was shocked to the core, and realized that Yugi changed hands so that when he drew a card, he would show Yami Yugi his own actions in his previous duel against Rafael.
"Alpha" attacks and destroys Yugi's Set monster, "Sangan" (1000/600). Since "Sangan" was sent from the field to the Graveyard, its effect activates, allowing Yugi to add a monster with 1500 ATK or less from his Deck to his hand. "Chimera the Flying Mythical Beast" then attacks directly (Yugi 4000 → 1900). Yami Yugi's hand is shown to contain "Dark Magician Girl", "Monster Reborn", and "Sangan" at this point.
Turn 5: Yugi
Yugi draws. He then Sets a card and activates "Card of Destruction", forcing both players to discard their hands and draw the same number of cards they discarded. Yugi then activates "The Seal of Orichalcos". From now on, all of Yugi's monsters will receive a 500 ATK boost. Yugi then activates his face-down "Monster Reborn" to revive "Dark Magician Girl" (2000 → 2500/1700) in Attack Position. Yugi then Normal Summons "Obnoxious Celtic Guardian" (1400 → 1900/1200) in Attack Position.
"Obnoxious Celtic Guardian" attacks and destroys "Alpha The Magnet Warrior" (Yami Yugi 4000 → 3500). "Dark Magician Girl" attacks and destroys "Chimera the Flying Mythical Beast" (Yami Yugi 3500 → 3100). Since "Chimera" was destroyed, its effect activates, allowing Yami Yugi to Special Summon "Berfomet" (1400/1800) from his Graveyard in Defense Position.
Turn 9: Yugi
Yugi draws. He then Tributes "Obnoxious Celtic Guardian" in order to Tribute Summon "Catapult Turtle" (1000 → 1500/2000) in Attack Position. Yugi then activates the effect of "Catapult Turtle" to Tribute "Queen's Knight" and inflict damage to Yami equal to half of the ATK of "Queen's Knight" (Yami Yugi 1200 → 200). Yugi then activates the effect of "Catapult Turtle" again by Tributing "Dark Magician Girl". However, Yami Yugi activates his face-down "Divine Wind" to negate the damage he would take, and inflict damage to Yugi equal to the damage he would have taken, plus 500 (Yugi 1900 → 0).
The duel was a test. By defeating Yugi in the Stone Wasteland, Yami Yugi was able to conquer the 'Darkness' within him and eliminate the malignant influence of the Orichalcos. Yugi pleads of him that no matter how much pain he suffers, he is not to be confused and believe in their bonds. He adds that Yami isn't alone anymore. The companions and Monsters he believes in will accompany him. Even if they're separated, Yugi will always be alongside Yami. Yugi's spirit vanishes and Yami cries in frustration and regret promising that he will save him no matter what it takes.
Except for The Seal of Orichalcos, Yami Yugi's and Yugi's respective Decks and Hands were in the same order, with the same Cards. Yami Yugi realized it early in the Duel, which is why Yugi changed his Hand. The "Seal of Orichalcos" Card was there because it was to show Yami Yugi what he'd done when he'd faced Rafael, though there was a slight difference.
The illusionary Yugi mentions that he knew that the day would come when he would have to face Yami Yugi in battle, and once Yugi defeats Yami Yugi, it will be their eternal goodbye. Both of these foreshadows the Ceremonial Battle they would have at the end of the series where Yugi faces Atem and defeats him so that Atem can finally move onto the afterlife.
It seemed "Dark Magician Girl" was aware of the duel as she looked distressed when forced by the seal unlike the other monsters (however, she didn't seem to fight it the first time she was under the seal as this is the second time).
Difference in Adaptions
In the original, Yugi instead said that Yami Yugi was arrogant, and that he cannot understand the suffering of others, whereas in the dub, Yugi instead said that he was evil.
At the end of episode, right after Yugi vanish, Yami Yugi yelled "Partner" in Japanese version. This was changed in dub where he said that he would save him no matter what.
In the original, when Téa inquires Ironheart if he had found Weevil's body, Ironheart announces that he entrusted him to some people he knew and was taken to the nearest hospital. In the dub, Ironheart states he found nobody else besides Téa and Yami Yugi in the wrecked train. This creates a plot hole in the dub as Weevil's body was later shown in the hospital that Rex and Alister's bodies were when their souls were returned to their bodies.