Yugi attempts to help Yami Yugi, but the latter tells him to stay back and that "this is [his] battle", in which he's staking his 'justice' and his 'beliefs'. Yugi gasps: Yami Yugi said the same thing in episode 158 when he used the "Seal of Orichalcos".
Yami Yugi tells him that this time it's different. He warns Yugi that, one day, they'll have to split and Yugi will have to handle on his own. And it's happening right now. Yami Yugi keeps on saying that they must accomplish his tasks. They're interconnected by everyone's thoughts.
Yami Yugi recalls the Duel he had with Yugi's spirit in the Stone Wastelands and Yugi's parting words.
By now, the "Great Leviathan" has become a blackish shape with yellow eyes, maybe meaning that it has lost part of its power and it's degrading into a more simpler form. It looms over Yami, apparently surprised at Yami's resistance. Yami claims that there's something inside of which cannot be erased no matter what.
Yami Yugi then announces that the container of memories which he built together with his friends won't vanish. It's the container of 'Light'. He then commands for the 'Dark' of the heart of this planet to vanish within this so-called container. The "Great Leviathan" tries to hold on, but it's eventually assimilated and destroyed.
And just in time, since the tsunami generated by the rise of Atlantis is just looming over New York City. It vanishes all of sudden, leaving the military men on board the aircraft carrier totally baffled: the commander wonders if a miracle has occurred.
The Light Returns
Ironheart, Chris, and Skye appear in spirit. They welcome back the spirit of Dartz, who thanks to Yami Yugi is no longer under the control of the Orichalcos God. Ironheart tells Dartz that Yami Yugi has shouldered all of Dartz's sins.
Ironheart tells Yugi & Yami Yugi to cross the portal: the future is awaiting them. They do so, and then Chris tells Dartz that they'll rejoin Iona's (Dartz's deceased wife and Chris' mother) spirit.
As Atlantis continues to crumble, the rest of the people in the temple flee since another tsunami is looming over it although Yugi & Yami are nowhere to be found.
Yugi wakes up on a deserted island, alongside Yami Yugi's spirit. "Dark Magician Girl" appears before them, along with the 3 Legendary Knights Timaeus, Hermos, and Critias. She thanks Yugi and Yami for their help: both worlds have been saved. She adds the following: "The souls of those whose flesh is already destroyed shall come back with us as well. I am sure that they wish to help build an idealistic world for the Duel Monsters to inhabit.". Yami also thanks the Legendary Knights for their help in making him get rid of his own 'Dark'.
The 3 Legendary Knights return to the Duel Monsters' World. They will always keep a watchful eye on the world when their help is needed again. "Dark Magician Girl" follows them.
The KaibaCorp helicopter arrives to pick up Yugi and Yami Yugi's spirit. Yugi knows that "Dark Magician Girl" wanted to add that, since Yami sealed the planet's curse inside of him, if he were to be stained by the 'Dark' of the heart again, the "Great Leviathan" would be able to come back. But Yugi is sure that it cannot happen and that Yami has achieved a new 'Light' and has become a true Pharaoh.
This concludes the Doma (season 4) story arc.
Differences in adaptations
The start of the episode is shortened - the original episode starts from around the last minute of the previous episode, whilst the dub episode cuts in before the second shot of Yami Yugi screaming as he endures the Great Leviathan's attack.
In the dub, Yami Yugi's flashback was different from the Japanese version.