It is believed that when all 3 Egyptian God cards, or the spirits of Slifer, Obelisk and Ra, are brought together under the lithograph, created by the Priest Seto as a reminder of his lost cousin, the brave Pharaoh, the Pharaoh shall regain his lost memories. The Pharaoh shall travel to his Memory World. A world of real, based upon the facts of Ancient Egypt, as is the memory. The Pharaoh will relive his lost days until he knows all, and then he shall know the truth...

After Battle City, when the carrier of the Pharaoh's soul, Yugi Muto, had obtained all 3 Egyptian God Cards from winning the Tournament, he headed to Domino City Museum where the Lithograph was held. He held up the 3 Cards but a powerful shock attacked him and he was unsuccessful. That turned into a war of Doom.

After Doom, Yugi tried again after school one day. The gang encountered Bobasa, a fat man with slots for each Millennium Item inside his skin, like an indent. Bobasa said that he was a member of the Tombkeeper Clan, and a servant of Shadi. When Yugi told Bobasa that he would not hand over his Puzzle, Bobasa lead them inside the building. The Pharaoh awoke and held up the 3 Egyptian God Cards to the Lithograph and began his past.

His friends on the other hand, including the soul of little Yugi, were still in the real world. Bobasa lead them into the chambers of the Millennium Puzzle, where they had to find the correct door, to gain access to the world of the Pharaoh's Memories. When they found the door, they entered it, unaware that a dark spirit was stalking them from the time he had entered the puzzle. Bakura entered the Memory World.

With things starting off as they should, Yami began his Memory. But this Memory wasn't a nice one. Bakura was back. The Thief actually... He appeared carrying the mummy of the previous Pharaoh, Yami's father, Akunamon. By this Yami challenged him to a duel, but Bakura's very own Ka, Diabound, was that of goodness, when he was clearly evil.

Yami's own Ka, Kuribo, wasn't good enough to stop him. But when he summoned one of his Egyptian God Monsters, the tables turned. Bakura fled, using Diabound's effect to move through walls. And the series skyrocketed from there. It deals with the facts about Ancient Egypt, previously introduced and adds a plot to them, including the famous duel of Yami and Bakura, Yami and Seto, and even the darkness that was featured within the sarcophagus at Kurelna.

The Millennium Ritual backfired, creating a being of pure evil, Zork Necrophedius. And with Zork and Bakura working together as one entity, the world is in grave danger.

But will the Pharaoh be able to stop it all? Or will the mystery lie in the lost name of the Nameless Pharaoh himself?