After being given the pieces of the ancient Egyptian artifact called the Millennium Puzzle by his grandfather, Yugi spent eight years attempting to solve the puzzle. When he eventually succeeded, he unknowingly undid a binding spell created by the ancient Egyptian pharaoh Atem, who had sealed the magic of the Shadow Games in the Puzzle and the other Millennium Items thousands of years ago in order to stop the victory of the evil demon Zorc Necrophades. The Pharaoh had bound the spell with his own name and sealed his own soul within the puzzle; when Yugi solved the puzzle, both the magic of the Shadow Games and Atem's soul were released, and Yugi's body became host to the spirit of Atem.
At first, Yugi has no awareness of the presence of this second personality within himself, which emerges in times of stress, takes control of his body, and punishes evildoers that threaten Yugi and his friends, leaving Yugi himself with no memory of the events. At the time, this personality - the true nature of which had not yet been divulged to the characters in the story - is referred to in Japan as Dark Yugi , in reference to the particularly sinister mannerisms of the pharaoh at the time, and the vicious punishments he meted out, including turning losing or cheating opponents insane. With the introduction of the Duel Monsters card game as the main fixture of the Yu-Gi-Oh! storyline, the "Dark Yugi" moniker no longer seemed appropriate, as the character ceased to be the sinister, vengeful figure of earlier installments. Now, he would emerge from the Millennium Puzzle to take control of Yugi's body for the purposes of dueling others in the card game; rather than entirely supplanting Yugi's personality, as he had before, there was a degree of interplay between the two, wherein Yugi was aware of his surroundings and the events of the duel, but unaware of the presence of the pharaoh guiding his hand.
After a contest with Ryo Bakura, in which Yugi's soul was removed from his body, he and his friends came to properly understand that an additional soul existed within Yugi's body when the pharaoh's soul, left in the body alone, took control of it and bested Bakura in their contest. This led to "Dark Yugi" being referred to as "the other Yugi" by Yugi's friends, and as "the other me" or "my other self" by Yugi himself. Additionally, Dark Yugi calls Yugi "partner" . When it was properly revealed that "Dark Yugi" was the spirit of the pharaoh, he became known as the Nameless Pharaoh , as his true name was unknown even to him, although everyone besides Yugi himself would refer to Atem as 'Yugi' nonetheless.
Solicitations and summaries for the English-language release of the manga consistently refer to the pharaoh as Yu-Gi-Oh, from the title of the series meaning "King of Games." Additionally, various English-language sources, notably video games, draw on the Japanese terminology and refer to the character as Yami Yugi. The English language translation of the series began referring to the character as Yami for the duration of the second season (perhaps to justify the "Yami Yugi" moniker without having to involve the Japanese language in the explanation), but this dropped early in the third season, and characters began to refer to Atem simply as "Pharaoh" without explanation to the sudden reversal of naming. On the other hand, Atem simply calls Yugi 'Yugi' instead of partner.
When the pharaoh takes control of Yugi's body, Yugi's undergoes a growth spurt, gaining additional streaks of yellow in his hair, and has differently-shaped eyes. Additionally, in the first series, Yugi's eyes were purple and Atem's were red. Also during the Duelist Kingdom arc, his shoes change when the Pharaoh takes over, from tennis shoes to what seemed like heeled boots. Whether or not such a transformation actually occurs within the fictional "world" of the series, however, is unclear, as no characters ever remark on his physical change, though some remark him as 'looking taller on TV'. Yugi's voice changes – in the manga, when the transformation happens in the presence of Anzu Mazaki (Téa Gardner in the English dub), who had her eyes closed at the time, the Pharaoh's voice was so different that she did not realize that Yugi was the speaker. In the English language dub of the first episode of the NAS/Studio Gallop anime, Seto Kaiba also notices a change in Yugi's voice. On several other occasions, other characters who possess Millennium Items are easily able to tell the two apart. In the 4kids dub, Yugi's thoughts whilst under the Pharaoh's control have the voice of Yugi himself instead of the Pharaoh (with the exception of the Doma Orichalcos arc, where Yugi's soul is captured), whilst in the Japanese dub (as well as the uncut English dub), the voice retains that of the current host.
Yugi has a mother and a father; his father is away on business, so Yugi does not see him, and his mother only appears very briefly. Yugi's parents were written out in the 4Kids dub.
Yugi's deck is well-known for the Dark Magician (Black Magician in the Japanese versions). At first it is composed of low-level Earth and Dark monsters with Spell and Trap cards to enhance them. Notable examples of his early monsters are Dark Magician, Giant Soldier of Stone, Summoned Skull, and Celtic Guardian. Later, during Battle City, Yugi acquires Dark Magician Girl, as well as his Magnet Warriors, Obnoxious Celtic Guardian, Buster Blader, Big Shield Guardna and Royal Knights, all of which become some of his most commonly-played cards. After winning Slifer the Sky Dragon, Yugi would usually summon the Egyptian God Card by special summoning all three Royal Knights and sacrificing the three monsters. Following Battle City, his deck slowly begins to focus more and more on the Dark Magician while maintaining a strategy to disrupt and disable his opponent's cards.
During the Ceremonial Battle, Yugi and Atem utilize decks that embody their own characters. Yugi's deck relies on the Magnet Warriors, Gadgets, and Level monsters, all of which combine powers and grow over time. Atem's deck relies on summoning the Egyptian God Cards, as well as the Dark Magician. In Yu-Gi-Oh! GX, Yugi's deck goes on tour at the academy, and is stolen by a copycat duelist. It was then later returned. This deck focuses on the Dark Magician, but also has several Chaos monsters. During his duel with Jaden in the past, Yugi uses a slightly modified version of the deck he used during the Battle City tournament.