Okay! Updated with my good Friend Arla Logan's beta'ing! Thank you so much for helping!
I do not own Yu-gi-oh, otherwise the end episode would never have happened.

It was night time, the time when, all should be sleeping. And all but two were. Those two, were Yugi Mutou and Yami. The two boys looked like twins because of their startlingly similar star-styled tri-colored hair. Yugi had amethyst colored, rounded eyes while Yami had crimson colored, box-shaped eyes. The most defining thing that marked them as not being related was the fact that Yami was a 5,000 year old spirit that lived within the Millennium Puzzle. Both were currently inside Yami's soul room, chatting away.
"But Yami, are you sure?" Yugi questioned his darker half borne from the millennium puzzle, worry evident in his features.
"Of course, Aibou. Nothing will go wrong." Yami smiled sincerely at his lighter half in hopes of easing his fears. Yugi nodded and his worry subsided for the moment.
"All right Mou hitori no boku." It had been established that there were not two Yugis, but he still liked to refer to Yami in that way. In a way it was a reminder of how they first met. With a glance, Yugi understood and left his soul room, willing his own soul back into his body and blinking wearily. He sat up and rubbed the sleep out of his eyes. He focused in when the puzzle glowed, drawing his attention. He grinned in anticipation and watched, remembering Yami's warning to keep a distance from the puzzle, just in case.
Within seconds the light shining from the puzzle grew too bright to look directly at, and he shielded his eyes and closed them so as to not go blind. He relied on his hearing, and he heard a faint hum that was oh so slowly growing in volume. After a minute of this, it stopped suddenly and there was a 'thud.'
Yugi blinked, lowering his arms and attempted to retrieve his vision that had momentarily left when the light got too bright. Only seconds had passed, and as soon as he was able to see again, Yami was the first thing he saw. He jumped off of his bed and went straight to his side.
"Yami! You did it!" Yugi whisper-shouted, mindful of his slumbering Jii-san. Yugi's grin was back, and he was hugging Yami, who was regaining his bearings. He had, after all, just used his Shadow Magic to create his own flesh and blood body outside the puzzle. It was new to him, having his own body and not just using Yugi's when he had to. The moment Yugi had slung his arms around him, he blinked, seeing Yugi's room through his own eyes. He smiled, then threw his own arms around his Hikari and hugged him.
"Yes, Aibou, I did." He confirmed. Neither took in Yami's lack of clothes.

~~~~~Morning~~~~~

Day time. Rushing around. The look-a-likes had almost forgotten Yami's accomplishment last night, until both had realized that Yami had slept on Yugi's bed and was currently running to school with him. The realization had both tripping over themselves and stopping halfway to school in the middle of the sidewalk to stare at each other. Yugi blinked, then both broke out in laughter. People glanced at them, wondering for their sanity, and passed by them quicker than when they had first spotted the hysterical look-a-likes.
Yugi came back to reality first and realized 'oh crap school starts in ten minutes!' He grabbed Yami's hand and dragged him off the rest of the way to school, laughter still bubbling from him occasionally because hell Yami got his own body!
When Yugi and Yami reached the school, everyone stopped and stared. The first ones to come out of it were their closest friends, Téa, Honda, Jou, and Ryou. Ryou, however, wasn't really noticed, since he was so quiet and just preferred to observe because holy shit the spirit of the ring was pure and utter evil! And said spirit tried to trap his friends in little figures and oh how he hated him!
Re-introductions were made, and realizations were discovered because heck Yugi was winning those games because Yami helped and holy hell how cool is that! Comment courtesy of Jou, of course. Yami had to go to the office to enroll if only to stay near Yugi 'cause fucking hell if he was going to abandon his Hikari just because the school wouldn't allow non-enrolled students to stay. One trip to the office later and Yami had received his schedule and acceptance into the school, and was currently on his way to his first class with Yugi. Happiness and joy was flying through the halls and spreading. The school was being contaminated with the pure joy the look-a-likes felt at having separate bodies and being able to touch the other without having to go to their soul room.
In their first class, history with Mr. Scile, the teacher, was an announcement of a new transfer student. He called the student into the room and told her to introduce herself. Her eyes, a jade green, roamed the class room, and she shyly introduced herself.
"Ah..I-I'm Seishin, Iah...um, I-I'm pleased to meet you all a-and I hope we can be f-friends..." She softly spoke and then Mr. Scile's directed her to a seat in the back right corner of the room, at the only open seat which just so happened to be next to Ryou. He felt a bit of pity for her, but put it aside and turned to the lesson. The rest of the day passed by quickly, as did the following months. The novelty of Yami having his new body wore off and everyday life hit them once more. It was around this time that Yugi noticed that his friends were ignoring him in favor of Yami. Yeah, he knew that Yami having his own body was new and awesome and holy fuck Yami used to be a fucking pharaoh?! He understood ignoring the guy they'd been hanging out with since Yami came into the picture. After the puzzle had been completed they swarmed him in favor of the apparent pharaoh that they knew about but didn't interact with much at all due to sharing Yugi's body.
Yugi started to become a little jealous, but hid it well since he realized quickly that his friends were only ignoring him because the novelty of a pharaoh being near was still affecting them. Yugi had been with Yami the whole time because of the situation they'd been put in, and understood the reasoning behind being in awe over Yami being there in the flesh. He smiled, waiting for the time when they would come down from 'Oh fucking hell there's a pharaoh here with us!' and acknowledge him again.
A year passed since that little 'revelation' and the others were still not acknowledging him. He didn't understand. What was wrong with him? They sure seemed to like being his friend when he and Yami shared his body.
Then it hit him.
Yami came into play after he completed the millennium puzzle. He made friends after Yami came into his life. People payed attention to him after Yami helped him get noticed. It all came down to Yami.
He understood in that moment, that everyone had always known about Yami ever since the beginning, and only hung out with him so as to hang out with Yami. If he hadn't of been at home, shut up in his room, he would have run to some more deserted part of the city to cry his heart out. As it was, he had to stifle his cries since Yami was home and oh like hell would he give him a reason to distance himself even more from Yugi. As it is right now he barely got any time to hang out with his Yami at all.
There was a knock at the door and Yugi pretended to have fallen asleep, head buried in his pillow so as to hide the tear tracks on his face. The door opens and he heard a sigh, followed by footsteps coming to his bedside.
"Oh Yugi, I know you're awake." Well there went that plan. He'd hoped that if Yami bought it, he'd be able to get out of the house without Yami knowing. He mumbled into his pillow, not wanting Yami to know he'd been crying because hell it would hurt to see the disgust on Yami's face at how childish he was acting and he couldn't stand it right now.
"Yugi? Sorry but I didn't hear you. Would you mind repeating that?" Yami asked, and Yugi decided to use the mind link, not trusting his voice at the moment not to crack and reveal what had been occurring not five minutes ago.
/ Yeah, I'm awake Yami. Is there something you wanted? / Yugi asked, careful not to let any of his sadness flow through the link. He knew Yami was smiling now, he didn't need to look up to know that Yami was smiling. After all the time they'd spent together, shared with each other, it was a wonder Yami didn't know what was going on.
/ Actually, Aibou, there was. A new burger restaurant just opened and I know that you love burgers so... / Yami didn't need to say, think or whatever any more, since Yugi immediately replied, cheering up at the prospect of hanging out with Yami and the others not being there to take all his attention from him. He sat up and grinned happily to Yami.
/ Sure Yami! Sounds like fun. / And I could do with a burger... he was careful not to let that thought go down the link. He didn't want to face Yami leaving him because he was too quiet to speak up and be acknowledged in Yami's group of friends. He smiled into the pillow and heard Yami leave the room, closing the door behind him.

/ I'll wait downstairs for you. / Yami replied, the smile evident on his face though he didn't see it. He nodded, though he knew Yami wasn't there, and carefully closed the mind link, not wanting Yami to notice that he had. While he changed out of his school uniform and into something more casual, he turned over the thoughts and revelations he'd had. Why didn't Yami's friends; yeah, Yami's, not his, he doubted that they even remembered him now that the real object of their attention was walking around in the flesh in blood; not want to be around him? Didn't they enjoy hanging out with him? I mean, I was always there, and they did interact with me more often than not...although they did ask about Mou hitori no boku quite often... were they ever truly his friends? On that thought, he left his room, dressed in a black T-shirt with a grey hoodie over it, black jeans with the pant-legs bunching slightly over his feet; they were designed to rest on top of his sneakers; and a smile on his face. He'd rubbed away all evidence of tears and quickly went into the bathroom to splash some water onto his face to get rid of the redness in his eyes.
While he dried his face, he silently re-opened the link, noting the fact that Yami didn't immediately get after him for closing it in the first place. Probably didn't even notice, he thought, glancing into the mirror and jumping slightly. He relaxed and chuckled to himself. It was just his own reflection, Yami was not there. Yami resembled him so much that he often thought it was Yami that he was and not himself.
Shaking his head, he headed downstairs to meet Yami at the door, smile in place. He blinked upon seeing the others there. He felt saddened that he wouldn't be noticed now, but refused to let it show and pretended his heart wasn't breaking a little more.

~~~~~ Time lapse ~~~~~

Yugi couldn't understand it! Why?! Why him? Why was it he was the one being shoved aside? Wasn't he a good friend? Wasn't he good enough? Wasn't he enough? Tears flowed freely, and he sobbed openly. There was no reason to keep quiet; Yami wasn't going to come check on him. It had been weeks since the outing to that new burger restaurant and Yami's friends had stolen every bit of his attention from him, so much so that even when they weren't there, Yami didn't pay attention to Yugi for even a second. He was too busy chatting with the others on the cellphone that Jii-san had gotten for him. He sighed heavily and turned onto his side, dulled eyes staring at the wall.
He couldn't find much motivation to get out of bed. He was far too depressed at loosing everyone to the one he was so close to. The worst part was that Yami didn't even notice it was happening, he thought, scowling at the wall. A knock at the door brought him out of his stupor.
"Yugi? Time for dinner." Jii-san said. That's right, Jii-san still liked him. He hadn't ignored him like his ex-friends did. A slight smile played onto his lips and he nodded, though he was the only one who noticed.
"Hai, Jii-san! I'll be down in a moment!" He called out to him. His door was locked all the time now, and he just knew that the door to his soul room was the same way. He didn't need to worry about anyone snooping for anything, not that anyone would. Jii-san was the only one who might, and he didn't snoop through others things. He heard Jii-san walks away, no doubt to the kitchen to set up the table for dinner, and he sat up. He wiped all evidence of tears away and went to the door, planning to dash into the bathroom. The lock clicked and he opened the door some, looking into the hallway for Yami. He really didn't want now to be the time that he decided to pay attention to him.
All clear. A sigh, and he walked into the hallway, closing his door behind him and walking to the bathroom. He splashed cold water onto his face, sighing. Why did this all have to happen to him? Why did he have to solve the millennium puzzle? Why did Jii-san give it to him? Just...why?
Another sigh, he seemed to do that a lot these days. Looking into the mirror, he scowled. He looked so much like Yami that it pained him to even look at his reflection. He sharply turned from the mirror and went down to eat dinner, a fake smile put into place to hide his despair.
All throughout dinner, Yami and Jii-san talked, although it was the latter who brought him into the conversations too. He almost had a real smile. It almost felt like none of that had happened and it was all just a bad dream that he finally awoke from. If only not for the fact that the depression he felt hurt. That reminded him that it was only because of his Jii-san that Yami was paying any sort of attention to him. Yami raised a brow at Yugi, and then the conversation continued.
After dinner was done, Yugi offered to clean up, much to Jii-san's gratefulness and Yami's non-acknowledgment. He sighed when they left the room and set about cleaning up the dishes. It was a quiet chore, the clinking of the dishes being the only sound. It was calming. And almost too soon were they done and put away. With a slight frown, he turned and went up to his room, calling out a goodnight before disappearing into his room. Only Jii-san replied.
Once he locked his door, he went right to his bed and pummeled his pillow, punching it so much that the seams started to rip. He stopped then. No need to have to explain to Jii-san why his pillow was torn apart and have to let him know everything about what Yami did to him, whether Yami realized he'd done it or not.

~~~~~Skipidy skip~~~~~

School, oh how he hated to be here. It was nothing but 'learn learn learn' all day until the final bell. And considering the fact that now the bullies were targeting him again, it was even worse. Right now even, they relentlessly let loose on him, until he was lying on the ground and there was some blood trailing down to the ground. They backed off then and went on their way, leaving him to his own devices.
He got up, shaking more from the beating than anything else that happened that day. Sighing heavily at his bad luck he went to the nurse to get looked at, grateful that she didn't pry. She gasped slightly at him; he knew he probably didn't look good but didn't care. He just continued to stumble to one of the beds and sat on it, sighing in slight relief. They must've twisted his ankle, as it had hurt to walk on his foot. The nurse quickly examined his injuries and wrapped them up. It was quick work, and he assured her that he was fine with continuing on to class. She didn't like the thought, he knew, but nevertheless, she let him go on to class.
History was his first class, and Egypt was the subject they were on right now. He didn't want to learn about Egypt. Yami came from Egypt and it was a hurtful subject. He grit his teeth and sat through the class, not noticing the gaze of the new girl. School couldn't be over quick enough. And the moment it was, he was off to his locker to leave the things he didn't need for homework. Noise flowed all around him, reminding him that he was all alone. Aside from the bullies, no one payed attention to him. It was saddening, and he moved quicker to get out of there. He was running, not willing to have the bullies go another round.
And so was his life, back to the way it was before, only worse off.