The pharaoh's memories had been carefully removed before the sealing to make sure he couldn't accidentally let slip his name and undo the seal. He was left with the idea of who he had been, and his knowledge of ancient Egypt, but otherwise he was empty. When the shadows came for him he was an easy target. He had no deal to save him, nothing to protect the gap left from his lack of Light. They shredded him tearing him apart for thousands of years until he had lost all of his identity, living almost as a shadow himself. He was stronger than them, and could command them, but they were vicious and had freedom he didn't. He was confined to a maze and didn't know why.
Shadi had left the Millennium Puzzle in the pharaoh's tomb, the Puzzle in pieces to be put together by the pharaoh's host when the time came. He was unaware of this. When he sensed something in the outside world the spirit would lash out viciously destroying those that would interrupt his sleep. He barely held back when he sensed something with an air of familiarity, a kind of magic similar to what was in the maze he lived in. He let the archaeologist take the Puzzle with him. Whenever the old man tried to give the Puzzle away or move away from it the spirit reacted violently, unwilling to leave the familiar man. The old man had retired after getting the Puzzle, not wanting to continue to risk his life when he was the only family his grandson Yugi still had. When Yugi was six he finally decided to give the Puzzle to him, a game to keep the boy entertained over the years.
Yugi wasn't very lucky. He attracted trouble as a pure Light. Receiving the Puzzle didn't help as his grandfather had hoped it might. Whatever dark powers the Puzzle might had seemed to be beyond his reach. Yugi was often beaten by bullies. His only friend was a girl, Tea, who he'd grown up with. She often didn't have time for him busy with studying to be a dancer and her dreams of a life in America. He was very lonely. His life turned worse as a teenager, two guys ganging up to tease and torment his odd hobbies. Joey used to be in a gang, Tristan from the same bad part of town but with a cop as his dad. Both were fighters, and both hated how weak Yugi was.
A bully targeted Yugi for Protection Fees, using Joey and Tristan as the example. Yugi stood up to the bully, willing to get hurt rather than see someone else hurt for him. The act spoke to the part of the guys that had bonded through fights and growing up in a tough neighborhood. They understood that hard headed loyalty.
Those thin bonds were enough when the Puzzle was completed to grant Yugi's wish. The shadows solidified the bonds between Yugi, Tristan, Joey and Tea to form them into friends and allies for the boy, unbreakable. Perhaps unnatural, but the bonds had been there, and Yugi now had his friends.
The spirit of the Puzzle was free now to do as he wished. He was thankful to Yugi for solving the Puzzle and granting him the ability to leave the room. The shadows had also backed off, warded away by the boy's Light. The spirit found it strange that he wasn't repulsed as the other shadows were but ignored it. He acted the part of protector to the boy. He didn't know much about this world, but he knew the Shadow Realm and it's magic intimately as a spirit born from it. He used his knowledge to destroy all the enemies in Yugi's way. Yugi's new friends were untouched by the spirit's actions as he could sense the shadow magic binding them to Yugi, and would never hurt his host. His protection extended to those bound to Yugi.
Yugi wasn't aware of what was happening at first. Strange things happened to those that would try to hurt him. He grew more and more fearful as time passed, finally becoming aware of another existence inside him. It was responsible for the death and insanity being unleashed.