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Atem wakes up on the balcony of the Palace, where Shimon Muran tells him the people are eager to meet their New Pharaoh. Although still stripped of his memories prior to sealing himself in the Millennium Puzzle, Atem greets his subjects.<ref name="mw duel 5">[[Yu-Gi-Oh! Millennium World - Duel 005]]</ref> [[Shimon Muran]] takes Atem to the Throne room, and invites him to sit down on this throne, calling it "The big gold chair right in front of you". Atem sits and upon seeing Shimon's face, (he was wearing a veil/mask prior to Atem sitting down), mistakenly calls him Grandpa because of his resemblance to Yugi's [[Solomon Muto|grandfather]]. Atem learns that there are [[The Sacred Guardians|six chosen priests]] in this world, who guard the [[Millennium Items]].<ref name="mw duel 5"/>

[[File:AtemWatching.jpg|thumb|left| Atem watching at the people around him]]He is quick to learn the Ancient Egyptian style of dueling. He witnesses the priests extract the ba from a criminal and seal it in a tablet.<ref name="mw duel 5"/> [[Thief King Bakura]] then arrives, after plundering the tomb of Atem's father, Pharaoh [[Aknamkanon]] and dragging the treasures and his corpse to the palace. Seto and Bakura Summon Monster Kas, which battle. Bakura's [[Diabound]] defeats Seto's dragon. He mocks Atem by trampling on his father's corpse. As the priests Summon more monsters to fight Diabound, Atem walks over and takes his father's body from Bakura. The priests desperately use their monsters to protect Atem as he does so. Atem steps in to avenge his father and summons [[Obelisk the Tormentor (original)|Obelisk the Tormentor]]. Obelisk battles Diabound. Bakura realizes he can't win, so he and Diabound flee.

Atem spots Bakura leaving the palace, after he had snuck in to possess [[Aknadin]] with [[Zorc Necrophades|Zorc]]. Atem chases after Bakura on horseback and battles Diabound, now powered by the Millennium Ring.<ref name ="mw duel 21">[[Yu-Gi-Oh! Millennium World - Duel 021]]</ref> Atem summons [[Slifer the Sky Dragon]]<ref name ="mw duel 21"/>, but Bakura is able to take advantage of Slifer protecting the civilians.<ref name ="mw duel 23">[[Yu-Gi-Oh! Millennium World - Duel 023]]</ref> Diabound manages to defeat Slifer and Atem runs out of ''Ba''.<ref name ="mw duel 25">[[Yu-Gi-Oh! Millennium World - Duel 025]]</ref> Atem's friends from the modern world, Yugi, [[Téa Gardner|Téa]], [[Joey Wheeler|Joey]] and [[Tristan Taylor|Tristan]] come to his assistance. Yugi combines his ''Ba'' with Atem's and together they summon the third [[Egyptian Gods|Egyptian God]], [[The Winged Dragon of Ra (original)|The Winged Dragon of Ra]].<ref name ="mw duel 25"/> Ra transforms into [[The Winged Dragon of Ra (Phoenix Mode)|God Phoenix Mode]] and manages to defeat Diabound<ref name ="mw duel 26">[[Yu-Gi-Oh! Millennium World - Duel 026]]</ref>, but Zorc, in control of Aknadin, reverses time, bringing back Diabound and pulling Atem's friends away from him. Without Yugi's ''Ba'', Ra leaves. Diabound shatters the ground below Atem, leaving him hanging off an edge. Here Bakura takes the [[Millennium Puzzle]] and leaves him to fall to his death.

At Kul Elna, Bakura tells Atem how the [[Millennium Items]] were created, by sacrificing the lives of the villagers of Kul Elna. He tried attacking Atem with the ghosts of the villagers seeking revenge, but Mahad, now fused with his [[Illusion Magician]] ''Ka'', returned from the dead as [[Dark Magician]]. The Dark Magician fends off the ghosts and battles Diabound. He assures Atem that his father had not known about how the Items were created. With the help of the priests and [[Mana]], Atem and Mahad defeat Diabound,<ref name="mw duel 41">[[Yu-Gi-Oh! - Millennium World - Duel 041]]</ref> but relinquish the [[Millennium Key]]<ref>[[Yu-Gi-Oh! - Millennium World - Duel 038]]</ref> and [[Millennium Scales|Scales]] in the process<ref>[[Yu-Gi-Oh! - Millennium World - Duel 040]]</ref>. Yami Bakura then freezes time in the RPG, allowing Aknadin, corrupted by Zorc, to gather the remaining Items off the other priests.<ref name="mw duel 41"/>

Using the Items Aknadin performed the ritual to Summon Zorc Necrophades, while Atem watched helplessly<ref name="mw duel 42"/>. Zorc attacked Atem and his companions, while they were still frozen, but Hassan arrived just in time to defend them from the attack.<ref>[[Yu-Gi-Oh! - Millennium World - Duel 044]]</ref>

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