People like to assume that Yuugi Mutou is stupid and try to take advantage of that, but he's a lot smarter than he likes to let on. So when people that he rather dislikes start getting hurt after he completes the Millenium Puzzle, he begins to take notice.
It had all started with Ushio, and Yuugi isn't quite sure what happened. The only thing he could remember was a knife, forty thousand dollars-twice as much as he actually needed-to pay the bully for his services (if you can call beating up Jounouchi and Honda, his almost-not quite friends for picking on him a profitable service), and the oppressive force of a glowing wadjet eye. He has a feeling that Ushio is in the mental institution because of him.
A few weeks go by and the next time something happens is when theres a celebrity in the school (there wasn't and that was the problem), needless to say Yuugi had gotten tricked into getting beat up for a commercial. He woke up a few hours later on his bed and a note on his desk that read 'You're Welcome' and Yuugi wasn't so sure how to feel about that.
When Anzu is held hostage a month or so later Yuugi can recall most of what happens. He doesn't however, remember how he gets her away from the convict. There's another note on his desk when he wakes up the next morning.
Months go by, and more incidents start to crop up, the severity of begins to lessen but Yuugi finds himself starting to worry about what's going on with him. Jounouchi notices this and instead of just telling him the truth like he should have, Yuugi just shrugs and tells him not to worry about it. Jounouchi worries regardless.
The amount of notes Yuugi receives grows along with his worry on the situation. After a few of them he had begun to reply. The replies he got were… interesting, apparently the reason he had been blacking out was his other self, at first he didn't believe it but after a long explanation and a trip to what his other self said was his soul room, Yuugi didn't have much of a choice but to believe him.
A few weeks after his other self-or Yami as he had taken to calling him-had revealed himself was when Seto Kaiba-President of Kaiba Corp-had transferred into Yuugi's class. After Seto had seen his grandfather's 'Blue Eyes White Dragon' Duel Monsters card and been refused his offer to purchase such a rare card, Yuugi knew he would try something. He was right, later that evening Seto had called, asking for Yuugi to bring the card to school so he could see it again, and sure enough he had attempted to swap the card with a fake.
Yuugi had expected Seto to feel guilty and return the card later in the day, but when he didn't Jounouchi and Honda had said something and gotten beaten up my Kaiba's bodyguards. Yami takes action and they duel, Kaiba doesn't play fair, and he uses the 'Blue Eyes' card that he stole. Yami does manage to win the card back; after that Seto Kaiba disappears for a while.
After a few more incidents Yuugi meets Shadii during the Egyptian exhibit at the museum.
His grandfathers old friend Professor Yoshimori is running it, but unfortunately his colleague Professor Kanekura was a greedy man and after displaying his puzzle in the exhibit for the day the man had tried to sell it, not caring if Yuugi was opposed-he didn't even tell anybody of this plan-to it. After the exhibit closes, when Yuugi goes to retrieve his puzzle, he is surprised to find an Egyptian man carrying it towards the entrance.
When he questions him, the man presses the tip of the golden key around his neck to Yuugi's forehead and stands like that for a good twenty minutes, Shadii-as he had introduced himself as-apologizes and returns the puzzle and as he leaves he thanks Yami for something and Yuugi doesn't see him again, but his other self does a few weeks later.
A few months pass before Yuugi runs into Mokuba, Seto Kaiba's younger brother, the boy had challenged him to a game of Capsule Monsters-Capumon-chess as an act of revenge for humiliating his brother, needless to say the boy had lost almost as bad as his older brother had and Yuugi doesn't see either of the Kaiba brothers until the Death-T event a few months-and a few incidents-later.
The Death-T had been part of Kaiba Land, an amusement park in the next town over. Yuugi's grandpa had been kidnapped and the only way to rescue him was to finish the Death-T challenge, Jounouchi and Honda had come along with him. Anzu had been the hostess for Death-T One, but decided to join them in the challenge, Honda gets trapped by the falling blocks in Death-T Three and Yuugi isn't sure how to deal with it.
He decides that now is a good enough time to tell Anzu and Jounouchi about Yami, they take it well enough but Jou' is a bit surprised at his other self's attitude. After Yami had defeated Mokuba in Capumon-again-Seto was waiting for him in Death-T Five, and just like last time Seto is defeated and Mokuba leads them to where his grandpa and Honda were being held, Yuugi almost starts crying when they all leave the Death-T Tower.
About three months after the Death-T event is when Ryou Bakura transfers into Yuugi's class, it turns out Ryou has an item like him, the Millenium Ring and it houses the spirit of an ancient tomb robber. Though nobody knows of this until he challenges Yuugi and friends to a tabletop RPG 'Monster World', Bakura plays at the Dark Master, and what he forgot to mention was that when their characters die, their souls are put into the figurines in order to continue. Yuugi all but demands that his soul is put into the game as well. Yami takes over his body and after a few hours of tiring struggle manages to-with the regular Bakura's-free their friends from the game and keep Ryou safe from the Spirit of the Ring, at least for a while.
Bakura comes to school a week later with a hand-made statue of Yami and his friends' 'Monster World' figurines and Yuugi thinks everything is going to be okay.