Yami Yuugi is the spirit of the ancient Pharaoh residing in the Millennium Puzzle. His past is shrouded in mystery.

3,000 (5,000 in the dub) years later, Yuugi Mutou, after trying to solve the puzzle for eight years, awakens the Pharaoh from his slumber, although Yuugi does not realize this until much later in the story.

At the end of Duelist Kingdom, the Pharaoh asks Yuugi to help him recover his memories and Yuugi agrees to help him.

Battle City
In Battle City, Yami discovers who he was in the past: He was a Pharaoh ruling in Ancient Egypt, according to Ishizu. In order to find out about his past as a whole, he must gain the three Egyptian God cards—Osiris (Slifer the Sky Dragon), God of Obelisk (Obelisk the Tormentor), and Sun God Ra (The Winged Dragon of Ra) during the Battle City tournament. Along the way, he runs into Noah, who has a grudge against the Kaiba brothers, and various pawns of Marik, his enemy in Battle City.

After Jounouchi collapses after his duel with Marik, or rather, his dark self, in the finals at Alcatraz Tower, Yami finds an even stronger incentive to duel him, but has to go through Seto Kaiba first. As expected, he defeats Kaiba and goes on to duel Marik, defeating him after an intense battle.
Doma Arc
In the Doma arc, things become more emotional for Yami. After he had failed to go into the Memory World due to the God cards 'not responding,' he finds that all the Duel Monsters have been turned into real life monsters. In his duel against Grimo, he finds out about the Seal of Orichalcos and its effect to take the soul of the loser of the duel. Unfortunately, after his duel with Grimo, his god cards are stolen by Raphael, Amelda, and Varon, people who work under Dartz's command. Dartz seems to be the new enemy of Yami's.

In his duel with Raphael, Yami is shocked to find the Seal of Orichalcos in his hand after he and Raphael exchanged cards due to a magic card's effect. In a desparate pinch, he activates the card, despite Yuugi's protests, and is under complete control. However, Raphael manages to defeat him. But before Yami's soul could be taken, Yuugi pushes him out of the way and his soul is taken instead, leaving Yami in a somewhat depressed state. However, Jounouchi quickly snaps him out of it by the form of a punch in the face, shocking everyone very much.
Memory World
After a historic battle against Zorc Necrophadius, he had sealed his soul along with Zorc in order to save Egypt. He had lost his memory as a result.

His real name is revealed to be Atem at the conclusion of the arc.