Changes

Joey manages to catch the last glimpse of YugiYami's Duel with [[Rafael]]. he He is astonished to see the symbol of the Orichalcos on YugiYami's forehead, since this must have meant Yugi Yami played "the Seal of Orichalcos"on his own. He witnessed Yugi This is nothign to his shock when he witnesses Yami lose the duel and watched him lose watches a soulbe taken. Rafael began to make his escape in a helicopter, taking Yugi's body with him. When Joey chased pursues and demands that Rafael give him demanding him to give Yugi back. , Rafael then flung Yugi's flings the body back at himdown. After Yugi begins to show signs of life, Joey becomes excited thinking Yugi had found a way to avoid losing his soul. But Yami Yugi revealed that only he had survived while "regular" Yugi let his own soul be taken. (In the Japanese version Jonouchi punched Yami for letting this happen and this . This was cut from the English Versionversion.)

Joey and Tristan get seperated separated from Téa and Yami Yugi, after when the train they were riding split in two. Outside the train , Joey and Tristan met meet Rex, who was is now working with Paradius and looking to duel Joey. Joey refused refuses to duel , knowing one of them would lose their soul if "the Seal of Orichalcos" was played. But Raptor began begins to duel anyway, playing the Seal on the first turn and left leaving Joey no choice but to duel back. Throughout the duel , Rex reveals his motive for targeting Joey. He and Weevil had been humiliated after their defeats to Joey and Yugi in Duelist Kingdom. They both suffered a mass loss in popularity and were now regarded as losers and a joke. He blamed Joey for all this, including going on to say Joey stole, not fairly won, his Red-Eyes. Joey proceeded proceeds to win the duel, causing Rex to lose his soul. He and Tristan were are left carrying Rex's body through the desert after this.

Joey's Hermos card began begins to glow as , and he sees the three [[Legendary Dragons]] appear and guide an airplane to crash land safely nearby. Joey and Tristan rush to the plane, where they meet up with Yami and and Téa, who had also seen the Dragons guide the plane. Kaiba emerged emergs from the plane, and he explained explains how Paradius had hacked into KaibaCorp and began taking over. Kaiba gave the party gives them all a lift to Domino City and left , leaving Rex in the care of his remaining faithful staff. The City had has become overrun with Orichalcos Soldiers. After being chased by one, Joey met meets [[Valon]], who took takes off on a motorcycle. Joey grabbed grabs a motorcycle that an Orichalcos Soldier had caused someone to fall off of and chased chases Valon. After catching up, Joey dueled Valonthey duel, while and Valon explained explains his reason for targeting Joey had been because of how ; from hearing Mai had constantly ranted rant about him and , he felt eliminating Joey would be a favor to her. However, Valon was becomes impressed by Joey's dueling skills and speech about how he felt dueling was about fighting for people you love. He soon came comes to respect Joey and saw see why Mai was is so interested in him. Mai appeared before the end of appears midway through the duel. She told , telling Valon off for dueling Joey because she wanted to be the one to defeat him. Joey won wins, and just before Valon lost his soul, he asked Joey to save Mai, before losing his soul.

Unable to convince Mai that she has been brainwashed, Joey said says the only way he could get through to Mai was to duel her. Through the course of the duel , Mai comes to remember why she had once cared for Joey. She holds back from attacking him when she is able to declare victory, but Joey still falls and the Seal of Orichalcos begins to take his soul. Mai rushes and hugs him to stop him from falling, telling him she was sorry and that he was "the closest friend she ever had.". Shorty Shortly after , Joey pushes her safely out of the Seal while his soul gets taken. An image of him standing, fists at his sides, appears on a tablet in Dartz's temple to show his soul's capture. (It is noteworthy that he is one of only two characters whose soul-carving does not look like he's panicking at his imprisonment. The other is Valon.) Mai weeps over Joey, denouncing everything she did. Once she calms down, she takes the Hermos card and rests his body next to Valon's before dashing to duel Dartz for Valon and Joey. YugiYami, Téa and Tristan arrive and take care of Joey's body.

Joey's soul returns to his body after YugiYami's duel with Dartz. Yugi returns Hermos to Joey , and he helps summon monsters to defeat [[The Great Leviathan]]. After the defeat of the Leviathan, he watches as the Legendary Knights and [[Dark Magician Girl (character)|Dark Magician Girl]] return to their world. The Hermos card fades away as he does so.