Changes
→Waking the Dragons
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]]" with "[[Berserker Soul]]". 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.
Yami and Téa are rescued by [[Ironheart]]. Ashamed of himself, Yami lets Ironheart hold onto his "Timaeus" card. Ironheart leads Yami to a place of lost souls, where, after confronting several evil spirits of Duelists he has faced (most of them originated in the Duelist Kingdom arc of this series), he finds Yugi's spirit. Yugi convinces Yami to engage him in a Duel, stating that this is the only way that Yami can prove he's sorry for his recent misdeeds. During the Duel, Yugi uses "The Seal of Orichalcos" which shocked Yami and a uses the strategy similar to Yami's from his Duel with Rafael. Yami tries to reason with him; but, Yugi refuses to listen and uses monster sacrifice to get through to Yami's doubts which is indeed a success by using a trap card, [[Divine Wind]] to counter this strategy. Defeating Yugi's strategy, Yami is told by his partner that he had overcome his mistakes and, in doing so, defeated the darkness in his heartand eliminating the influence that corrupted him. As Yugi vanishes suddenly, Dartz conjures an Orichalcos Soldier to duel Yami immediately afterwards. Yami is unable to defeat the Soldier's "[[Orichalcos Gigas]]" without "[[The Eye of Timaeus|Timaeus]]", so Ironheart, [[Chris]] and [[Skye]] sacrifice their own lives as they return the card to Yami, imploring him to save this world. With the darkness within Yami's heart erased, he summons "[[The Eye of Timaeus|Timaeus]]", fuses his dragon with "[[Dark Magician Girl]]" to summon her "[[Dark Magician Girl the Dragon Knight|Dragon Knight]]" form, and uses it to defeat the Soldier.
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 her soul. Yami makes his way to Duel Rafael, who tosses him Joey's "[[The Claw of Hermos|Hermos]]" card. This time Rafael uses "[[The Seal of Orichalcos]]" and allows his "[[Guardian Eatos]]" to fall under its power. However, after Yami uses "[[Amulet Dragon]]" to destroy "[[Guardian Eatos|Eatos]]", "[[The Seal of Orichalcos]]" begins to feed on Rafael's anger, just as "[[Guardian Dreadscythe]]" is summoned in [[Guardian Eatos|Eatos']] place. Equipping his new Guardian with his "[[Reaper Scythe - Dreadscythe|Reaper Scythe]]" card, Rafael defies his own practice of letting his own monsters go to the Graveyard in a vengeful attempt to defeat Yami, stating that he hates him more than the thought of having monsters in his Graveyard. However, after Yami summons "[[Guardian Eatos|Eatos]]" back to the field under his control and equips her with "[[Goddess Bow]]", he destroys Rafael's "[[Guardian Dreadscythe|Dreadscythe]]", ultimately managing to free him from Dartz's influence. To end the Duel, Rafael plays "[[Soul Charge]]" to revive his monsters, but depletes his Life Points and loses on purpose. However, since Rafael overcame the darkness in his heart, there was nothing to power the [[The Seal of Orichalcos|Seal]], thus allowing him to keep his soul.
