Pharaoh Atem is the spirit residing in the Milennium Puzzle. After a historic battle against Zorc Necrophadius, he had sealed his soul along with Zorc in order to save Egypt. However, he had lost his memory as a result.
3,000 (5,000 in the dub) years later, Yugi Mutou, after trying to solve the puzzle for eight years, awakens Atem from his slumber, although Yugi does not realize this until much later in the story, more specifically, Duelist Kingdom.
At the end of Duelist Kingdom, Atem asks Yugi to help him recover his memories and Yugi agrees to help him.
Battle City
In Battle City, Atem 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, Atem 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 Atem. 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 Atem's.
In his duel with Raphael, Atem 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 Yugi's protests, and is under complete control. However, Raphael manages to defeat him. But before Atem's soul could be taken, Yugi pushes him out of the way and his soul is taken instead, leaving Atem 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.
