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MAJOR SPOILER WARNINGS, I REPEAT, MAJOR SPOILERS

After the adventure in the memory world Atem discovers his true name (A-TE-MU) , Isis tells him that this is final key and she, Malik and Rishid take Yuugi-taichi to the stone tablet that holds the passageway. All Senen items are presented on tablet, God cards and Pharaoh's true name.
Final step is that Atem must loose in holy duel, Katsuya offers to duel him but Kaiba says he is an underdog, Katsuya is upset but backs down. Seto then says that he will duel Pharaoh and when Atem refuses Kaiba threatens him. Instead Atem chooses to duel Yuugi.
In holy duel Atem sumons all three God cards, no one knowns how to defeat them for they have never been summoned all at once by one player before. (This is where American movie contradicts original0 Even Malik, who knows secrets of Ra better than any other doesn't know how to defeat them all.
I don't know how, but Yuugi defeats Atem and he goes to the world of the dead. Final scene in manga is of Yuugi-taichi looking up at the sky after escaping the place where Yuugi duelled Atem as it began to crumble.
So ends Yu-Gi-Oh.

There is a notion of a Next Generation, however, none of the old characters will be present, Duel Disk systems are different and to be honest, how can you follow up an ending like that?