Okay, here's something weird again inspired by my sister (great source of inspiration for fanfics). Mostly based off the manga, but some events from the anime get merged in. Might have a sequel later. I don't own Yugioh because things would be way different if I did if this is any indication.
Yugi couldn't tell you why, but he always felt like he was being watched. When he turned around, however, there was nobody there. It's an eerie feeling, to be watched all day. Even in his own bedroom, which should have been private. The funny thing is, this feeling didn't come until after he solved the Millennium Puzzle. Once he had completed the ancient Egyptian artifact, he never felt alone.
At first, he thought it was just the spirit inside of the puzzle. At least, after he met the spirit. But at Duelist Kingdom, when he and the spirit—Yami, as Yugi called him—had first communicated through their minds, Yami revealed that he felt as if they were being watched as well. That first night on the island was an eerie one, and not only because of the player killer, Panic, but also because of the sounds that he heard; the girlish giggling at Yami's taunts, the cries of fear and rage whenever Panic threatened him. Those sounds didn't come from his friends watching on the sidelines—they weren't made by anything human, he and Yami agreed. So what was watching them?
Aside from the eerie feeling of being watched, he normally felt nothing odd. Except on rare occasions. Such as the day he played Dungeon Dice Monsters with Ryuji Otogi over the Millennium Puzzle. The growls that emanated from nowhere were not only terrifying to Yugi, but to his opponent as well. At one point, Ryuji's dice had even taken it upon themselves to attack his father, right after the man in question had shattered the Puzzle. The dice flew off the table, straight for the man's head; and as Ryuji tried to solve the Puzzle, there was a sort of mumbling in a language Yugi couldn't understand.
Battle City proved even more horrifying in regards to the strange presence. Over time, Yugi had grown quite fond of the spirit within the Puzzle, but the one that followed him had yet to even reveal itself. When Yugi was reluctant to let Yami regain his memories, the unknown spirit had retaliated; Yugi woke up one morning with strange markings on the wall in what appeared to be blood. Too afraid to find out, he had simply washed away the markings. As Battle City began, the second spirit calmed down—Yugi would learn later that Yami was in the tournament for the sole purpose of regaining his memories, which had seemingly calmed the other spirit. As the tournament wore on, strange things continued to occur.
The strangest event had to be the one that happened during his duel with Pandora. After Yugi's Dark Magician had been defeated once and for all, Pandora used Dark Magic Curtain to summon another of his own Dark Magicians. Yami had used the card's effect to summon the Dark Magician Girl, the monster's debut in their duels. Something about the holographic image had seemed off though. The gleam in her eye had been so lifelike that Yugi had wanted to toss the card right then and there. If it hadn't been for Yami's protests, he would have.
Every time that the Dark Magician Girl was summoned, the same thing happened. And when the Dark Magician Girl was on the field, Yugi no longer felt as though he was being watched. It was as if the unknown spirit that followed him everywhere took on the form of the Dark Magician Girl whenever Yami summoned her. This wasn't something Yugi could ever explain; he didn't understand it himself, after all.
The spirit didn't appear in the holographic image of the Dark Magician Girl anymore after Battle City, but Yugi often felt that the spirit was waiting impatiently for something. The day that he went to the museum in search of Yami's memories—and wound up having issues with Dartz instead—the spirit had seemed eager, excited. It was as if it was waiting for Yami to regain his memory. Disappointment and anger were the emotions it radiated after the first attempt failed. Rage was the primary emotion that Yugi felt from it during the Dartz incident, although Yami told him that this had turned to sorrow and pity after his duel with Raphael where he used the Seal.
And don't even get Yugi started on the Kaiba Corporation Grand Championship. The spirit didn't approve at all. Apparently, it wanted Yami to hurry up and regain his memories, so it was furious with the both of them for deciding that a few more days wouldn't hurt.
Sadly, when Yugi finally did return to the stone slab so that Yami could regain his memories, it was almost a relief. The unknown spirit wasn't angry with them anymore, although Yugi could sense that it was still annoyed with the pair of them. Once Yami had gone to the World of Memory, the other presence vanished as well. For the first time since he had solved the Puzzle, Yugi was alone... and he didn't like it. There are no words to describe Yugi's feelings when he learned that he could go to the World of Memory along with Yami and help him.
Later, in the World of Memory, Yugi saw a girl by the Nile. She looked strangely familiar, which was odd since this was ancient Egypt; the only person he should have recognized should have been the pharaoh, Yami. However, getting a closer look, Yugi realized that this girl greatly resembled the Dark Magician Girl. When she saw them, she remarked on how the pharaoh had shrunk and asked why he was wearing such strange clothes. Looking into her eyes, Yugi felt something familiar. It took him a long time to realize what it was—only after she and the pharaoh had left for the village of Kul Elna did Yugi realize: That was the other presence, the other spirit.
He didn't have time to dwell on it at the time, but later Yugi would wonder why Mana, the pharaoh's friend, had been haunting him for so long. Why was she following the pharaoh's soul around the modern world? Yami—or rather, Atem, as his real name turned out to be—wondered the same thing. The presence wasn't nearly as strong in the last month before Atem left for the afterlife, but there was no doubt that she was still there. Apparently, she was trying not to draw attention to herself anymore; when Atem tried to speak with her, her presence vanished completely and didn't return for several hours.
As he stood in the underground chamber, ready to duel Atem to send him on to the next life, Yugi realized that he may never know why Mana was haunting him. However, it became slightly more clear as the outcome of the duel failed to be what it should have been: Yugi's Monster Reborn had been replaced with a Premature Burial, essentially the same effect, but not the same card. Slifer was reborn, and Yugi lost. Atem was trapped in the Puzzle. And Yugi knew that it had to be Mana's fault.
How could she do this to him? Yugi wondered on the plane ride back to Domino. She was supposed to be his friend!
Atem wondered as well; he knew that the duel had been manipulated by an outside force. He had sensed something strange just before Yugi revealed his card. But, unlike Yugi, Atem was still more concerned with Mana's presence here period. Why hadn't she moved on? Surely, as a priestess, she had been interred properly. So why was she still here? As the plane landed, Atem realized that he may never know the answers, unless Mana one day decided to reveal them.