Bakura tries to escape the returning spirit of the Millennium Ring, Yami Bakura, who tells him they still had to obtain all of the seven Millennium Items. At the moment, they had only one, the Millennium Eye. When Bakura refuses to help, Yami Bakura forcibly takes over his mind and body.

Seto and Kisara face Aknadin, however Kisara is killed while protecting Seto, and the White Dragon is sealed in stone. Meanwhile, Yugi and his friends brave many deadly traps finally find the Pharaoh's true name in a room in the back. The Pharaoh makes it back to the palace, however he is forced to battle against Seto as his mind was being manipulated by the evil Priest Aknadin. The legendary ancient match between the Pharaoh and Priest Seto begins. The Pharaoh summons Mahad, as Dark Magician, to fight against the Blue-Eyes White Dragon, now controlled by Priest Seto. The Pharaoh is eventually overpowered. However, the spirit of Kisara, in the form of the Blue-Eyes White Dragon, enters Seto's mind and destroys Aknadin for good. As a result, Aknadin's soul is sent to the Shadow Realm. However, the time on Yami Bakura's 3rd hourglass runs out, and Zorc Necrophades begins to revive.

Thief King Bakura succeeds in reviving Zorc Necrophades, sacrificing himself and his Diabound in the process, the two absorbed into the Millennium Stone. As Zorc emerges from underneath Kul Elna, his energy destroys the Millennium Stone, causing the Millennium Items to scatter throughout Kul Elna. The Pharaoh and Priest Seto ride back to the palace and attempt to stop Zorc. Shada intercepts a lightning bolt sent by Zorc meant for the Pharaoh and dies. Meanwhile, events in the Memory World have linked to the Real World. Zorc's revival causes the Real World to be beset by all sorts of natural disasters. Once Yami Bakura gains the Pharaoh's name, he intends to revive Zorc in the Real World.

Isis and Mana head for Kul Elna to retrieve the Millennium Items. Isis uses her Millennium Necklace to strengthen her Winged Guardian of the Fortress to distract Zorc. However, Zorc destroys Isis's dragon and the amount of damage she takes kills her. Once Mana delivers the Millennium Items to Shimon, he summons Exodia with the Millennium Key, which holds its own against Zorc. Zorc eventually overpowers it, since Exodia drew its power from a mortal, Shimon, while Zorc had an almost infinite supply of darkness. Zorc the Dark One then destroys Exodia, killing Shimon. Mana delivers the other Millennium Items to the Pharaoh, who prepares to fight Zorc.

The Pharaoh summons the Three Egyptian Gods to combat Zorc. At the tabletop in the Shadow Realm, Yami Bakura claims he'll soon return to his original form, and leaves the table to join with his 5,000-year-old counterpart — Zorc. At the same time, he sends the present-day Pharaoh to the battlefield to reunite his past self. Meanwhile, Zorc defeats the three Egyptian Gods by covering the Sun, the source of their strength. Zorc then turns the Egyptian Gods into motionless statues of stone.

Yugi tries his best to fend off the attacks from Atem's most faithful servant, the "Dark Magician", but he is left with just 400 Life Points remaining. Yugi then plays a Spell Card, "Gold Sarcophagus", which allows Yugi to choose any magic card from his deck and store it in the chest; if Atem ever uses the same card himself, then Yugi can negate the activation of that card. Yugi tries to use "Gandora The Dragon of Destruction" to defeat the "Dark Magician", just how he was able to defeat Yami Bakura, but to no avail. Atem summons his "Dark Magician Girl" to support his "Dark Magician" in response to Yugi summoning his "Silent Magician". Yugi forces Atem to sacrifice both of his magicians to protect his Life Points after Yugi uses "Card of Sanctity" to increase the strength of his "Silent Magician". Atem then tries to activate the Spell Card, "Monster Reborn", so he can revive "Slifer the Sky Dragon", but at that moment, Yugi opens the Gold Sarcophagus to reveal the card he sealed away. The card was "Monster Reborn", meaning that neither of them can use that card in this game. It is Yugi's message to the Pharaoh that "Those of the dead should not remain in the world of the living". With the activation of "Monster Reborn" negated, and Slifer the Sky Dragon sent back to the graveyard, Atem is left defenceless. Yugi finally defeats him, but immediately collapses on his knees in tears, distraught at the realisation he will never see Atem again. Despite Atem telling Yugi that he shouldn't cry, Yugi tells Atem that he (Yugi) is weak, and that Atem's strength and bravery was always his goal. Atem comforts Yugi, saying that he displayed true courage in even deciding to duel Atem in the first place, and that he had a power that no-one else could conquer: that of kindness. Yugi's victory has finally set him free. Atem then departs into the afterlife. Then, the Millennium Stone shatters, which causes the seven Millennium Items to fall into the pit left behind. Also, the shrine collapses, and Shadi's spirit is seen here one last time. Everybody barely makes it out in time. As a result of the shrine's destruction, the Millennium Items are buried forever. Yugi tells Joey that, "Sometimes, the end of one adventure is only beginning of another." This concludes the end of the 4-Kids version of the story.