Ryo Bakura's soul was destroyed along with the dice. Yami Yugi won and gained the next key card. The Yugis were brought to the Shrine of the Millennium Stone by Marik, Ishizu and Rishid. If not, they would be expelled and the tester would be smashed. Everyone chases him into the room and they find themselves in an alternate dimension. Mokuba was stunned to see that Yami Yugi rescued him. Mokuba then went to ask Yugi and his friends for help. Stardust Dragon's first attack almost destroys Neos and sends the two skidding backwards into a wall. Atem then led the troops to Kul Elna to confront Thief Bakura, where he wouldn't be able to kill innocent bystanders. Paradox knew that he would try to go for the "Dark Magician". That was what he could show, but could not see. In the meantime, Yugi has recovered, and Tea shows the Pharaoh the trial's instructions. Yami Yugi faces Mai in the first round of the finals, but patronizes her and only thinks of facing Pegasus. However "Rogue Doll" being destroyed on the tape's footage indicated Pegasus knew that would happen when he made the tape. Yami Yugi and Joey had to take turns tossing the Millennium Puzzle. Yami Yugi defeated the first dragon, by hiding his monsters with "Magical Hats". Yami Yugi agreed, but offered to take over if the need arose, and wished his partner good luck. As they proceeded to the next stage, Joey picked up a "Booby Trap" card, triggering a trap, separating Joey and Tristan from Yami Yugi.

Another message arrives, and Solomon reveals that next is "The Trial of Light and Shadow". After escaping the Virtual World, Yugi and the other three finalists in Battle City—Yami Marik, Joey Wheeler, and Seto Kaiba—competed against each other in a 4-way Battle Royal, to determine which opponents would be paired up against each other.

He explained that Pegasus had wanted to take over KaibaCorp so he could use the Solid Vision technology to create a lifelike vision of Cyndia. However, it can't due to another Later that night, a group of perpetrators broke into The next night, when Yugi falls asleep, he and Yami awaken inside the Millennium Puzzle, where Afterwards, Pegasus sends Yugi and his friends a videotape, inviting the group to Yami falls into depression and guilt over what he let happen to Yugi. However Yugi says Atem was alright, and is doing just fine after seeing Yugi again.

After Yugi and his friends evacuate the aircraft, they find a man who says his name is Dr. Alex Brisbane. Yami Yugi retook control after Yugi vowed to destroy the embodiment of Yako's wrath.

Kaiba would ultimately force the Duel into a 6-turn showdown by using "Final Attack Orders" to reduce both players' Decks to 3 cards.

Yami Yugi manages to destroy "Obelisk" and defeat Gurimo, sealing Gurimo's soul, but does not recover the God cards.

Yami then activates "Dark Spiral Force". Yugi, unable to cope with the Shadow Realm passes out after a few turns, setting a card as he does so. Isis and Mana set off to retrive them. Yusei is stunned by this, to which Paradox says that he is not the only one who could Synchro Summon. He would even tell his enemies to surrender the duel for their own safety, an example being during his duel with Arkana. Yami summons the Egyptian Gods, thinking it will be enough. Also like Yugi, Yami Yugi has have a long lasting friendship relationship with many duelist that he fought in the series. Yami Yugi suspected Mokuba was cheating when he saw how he could eat a meal without any fear of it being poisoned. After talking with Mai about facing fears, Yugi lets Yami take control.) The slabs represented a mirror and Yami Yugi needed to determine what the odd image was within five minutes or be bitten by Ammit, which despite being an illusion would kill him. Because of the effect of "Malefic Paradox Dragon", the ATK of "Elemental HERO Neos Knight" is reduced to 0. He would help out others, and try to search for his friends. the Skull Guardian, but to show mercy. 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. This shows that Mokuba cares about Yugi's well being. Imori created a flood with "Shui Long" in an attempt to rust "Jin Long". Pegasus is finally able to land and arrive at the event. In Yu-Gi-Oh! Shadi introduced himself as an unwanted guest, who had come to learn the power of the Millennium Puzzle and if the power was needed he would draw it into his bloodline. Mokuba then sees Yugi battle Yami Yugi in the ceremonial Battle. Though the gods were able to overpower him, it did not last.

You obviously do not know much about the names in the original series. Jonouchi was startled but reassured and returned to his own dimension. Inside, Yami observes with interest the many games he has never heard nor seen before. Yami is unsure if that's the safest option, but relinquishes control to Yugi. He manages to lure Yugi into a Duel, but tells him he won't be using "The Seal of Orichalcos". With "Wild Spider" on the floor, Nagumo's field monster was replaced with his own soul as punishment for betraying the trust of his monster. Yami convinced Noah to Duel him after he said that Kaiba would have beaten Noah, had Noah not used Mokuba to keep him from losing.

Yugi went to Domino Stadium for the finals, where he boarded the Battle Ship blimp, along with the other finalists and his friends. As Yami Yugi is angry about Joey's loss.