I just thought about this story, and it doesn't go with the current universe that I have created but it came to me.

It can of goes, but in a different sense. 

What if Yami, Yugi and the rest of the gang didn't know that Pegasus had Mokuba?

Never Knew

Part 1

     A slender figure walked gracefully down a torch lit corridor.  He had been called by the mad man that was in charge of the whole island. 

     The beautiful blue eye young man had been attacked in his own home, by the lunatic's henchmen. 

     He was about to get away, when one of them informed him that Pegasus had his little brother.

     He didn't what to believe it, but when it came to Mokuba, Seto could not, would not take any chances.

     Seto continued to walk down the hall where the goons had pushed him in to, instructing him just to keep walking forward.

     Seto narrowed his eyes, when he saw a white hair man in an orange colored suit standing before him with a card in hand.

     "Kaiba boy, I knew you would come," Pegasus smiled.

     "Seto," a tiny familiar voice called him causing his eyes to widen.

     "Mokuba," Seto called and rushed to where Pegasus stood to notice that he was standing next to a cell, and his little brother was in it.

     "Seto, I knew you would come for me," Mokuba smiled.

     Seto smiled a smile that was only reserved for his little brother.

     He turned to look at Pegasus who was grinning.

     "You should smile more offend," Pegasus stated.

     "What do you want?" Seto demanded.

     Seto saw Pegasus smiled before a flash of light blinded him.

     He opened his eyes, to see the in Pegasus's hand now had a picture of Mokuba on it.

     "What is this?" Seto hissed and looked back at Mokuba.

     "Mokuba?" Seto called but there was no answer.

     Seto kneeled down to look at his little brother's eyes.  They were lifeless and empty.

     "What have you done?" Seto demanded.

     "You see this card in my hand, Kaiba boy.  It contains your dear little brother's soul," Pegasus smiled.

     "You're lying," Seto stated.

     "Oh really, so you wouldn't mind if I ripped the card in two," Pegasus stated.

     "No," Seto shouted.

     "What do you want?" Seto echoed his earlier question.

     "Your company and you," Pegasus stated.

     "What?" Seto asked confused.

     "I'll make you a deal.  Little Yugi and the Spirit of the Puzzle our on their way here to battle me, I want you to battle them first and win.  If you win I will give you back Mokuba," Pegasus stated.

     "And if I lose?" Seto asked.

     "Then you never see your little brother again," Pegasus answered and was about to walk away.

     "Wait, I want to make a change in the deal," Seto said.

     "Oh, what?" Pegasus asked.

     "If I lose, you let Mokuba go and I take his place," Seto stated.

     "You would give yourself up for your little brother?" Pegasus asked.

     "Yes," Seto answered in a heartbeat.

     "Fine then, win Mokuba goes free, lose you take his place," Pegasus smiled and turned.

     "Come now, the battle will begin," Pegasus said as he walked.

     Seto turned to look at Mokuba's soulless body one more time before he followed Pegasus.

     He listened to Pegasus ramble to what to do and where to go to battle with Yugi and what not.

     He followed thinking things over in his head.

     He's crazy.  There is no Spirit of the Puzzle, Yugi battles alone.  But then again Yugi always looks different when he battles.  He's more confident, stronger, he even looks taller.   He always looks innocent but during a battle he looks more mysterious kind of exotic.  Exotic what am I thinking, Seto thought.

     He shook his head and stopped in front of a pair of doors.

     "Yugi and friends are going up the stairs as we speak, remember our deal, Kaiba boy," Pegasus smiled and walked away.

     Seto looked back at the doors as they began to open.

     The group had been walking up the stairs.  Tea was close to Yugi talking about how proud she was of both of Yugi and Yami.  Tristan, Joey and Ryou were walking behind them.

     Yugi would sneak a glance back at Ryou every now and then.

     He could help but remember everything that happened two nights ago when they defeated his Spirit of the Ring, who was going by Bakura.

     Yugi had noticed Joey was kind of sad after that but he thought it was best if he didn't mention it.

     Last night while everyone was sleeping, he and Ryou where off by themselves, talking about their millennium items.

     There was a cold wind and Yugi could help but shiver.  Ryou got close to keep him warm, and Yugi felt so safe with him.

     The next thing he knew, he wrapped in Ryou's arms kissing him softly, while Ryou had placed him on his lap.

     Yugi couldn't help but blush at the thought; a noise had separated them and awoken the others so they didn't have much time to talk about it.

     The noise sounded like a helicopter but they didn't see where it went to.

     "Thinking about your love interest?" a voice asked.

     "Yami, Yes, no… Stop teasing me.  I don't tease you about Kaiba," Yugi stated.

     "Because there is nothing to tease me about, Yugi," Yami stated.

     "Yes there is.  You find him fascinating," Yugi stressed the last word.

     "Well he is a fine duelist," Yami stated.

     "That's not all you think is fine about him," Yugi laughed.

     Yugi stopped his mental conversation with Yami when he heard and saw the doors at the top of the stairs open.

     The group was in shock when they saw the one and only Seto Kaiba standing in front of them.

     "Kaiba, what are you doing here?" Joey demanded.

     "None of your business, mutt.  Yugi Motou, I'm your finally challenge, defeat me and you move on to battling Pegasus," Seto said.

     "Kaiba, you're in on this too," Yugi asked heartbroken more for Yami than for himself.

     "I don't know what your talking about, are we going to duel or not?" Seto asked.

     "Yes," Yami answered in a different voice.

     Seto noticed it, but put it a side.

     "Follow me," Seto stated and walked were Pegasus had told him to.

     As they set up for battle, Yugi kept telling Yami how sorry he was about Seto, but Yami only replied it meant nothing he would just have to teach him all over again.

     "I should have known, Kaiba was in on this," Joey stated.

     "I guess he is a heartless machine," Tea frowned.

     Seto ignored there comments not having one single clue to what they were talking about.

     Not knowing that Yugi had a reason like him for being here, he didn't know Yugi's Grandpa's soul was taken as well.

     As soon as the battle started, Seto concentrated on creating something he had thinking about. 

     Every turn he made he put all of his heart and soul into, but apart of him didn't know why it felt wrong.

     Yami had noticed that every moved Kaiba made was very careful thought out, almost as if his life depended on it.

     In the heat of the battle, they all failed to notice all the eyes that were on them.

     And at the end there was only one winner.

     "Sorry Kaiba you lose," Yami stated proudly.

     Seto had been a tough opponent he was even better then before and his creation was pure genius.  He would have never thought of combining all three of the Blue Eyes White Dragons together to make an ultimate one.

     He truly was Yami's rival.

     Seto closed his eyes and fell to his knees, he had lost.

     He lost, but at least Mokuba would be free, but who would be there with him.

     "No," Seto sighed as he buried his head in his hands.

     "Come on, Kaiba, don't to be a sore loser," Tea stated.

     Yami was about to comment something when Seto stopped him.

     "Pegasus, we had a deal," Seto shouted.

     "What you made a deal with Pegasus, that he could get you to beat Yugi, that's pretty low," Joey stated.

     "Shut up you mutt," Seto shouted to the group.

     They were taken back when they noticed tears coming from his eyes.

     "Kaiba…" Yami started

     He stepped forward but stopped, when he heard a voice.

     "Big brother," a child came running to them.

     Seto looked to see Mokuba running to him, and he couldn't help but smile.

     Mokuba ran to Seto and jumped at him and hugged him tight.

     "Seto I knew you would save me.  I knew you would keep your promise," Mokuba said as he continued to hold him.

     "You remembered," Seto whispered.

     Mokuba smiled and nodded. 

     The group stayed silent as the scene was unfolding in front of them.

     Seto stood up from as little brother's embrace and smiled at him.

     "Seto," Mokuba stated as he saw the tears coming from his eyes.

     "Seto what's wrong?  Let's go home now," Mokuba stated.

     Seto smiled but tears continued to fall.

     "Mokuba, I want you go one of Pegasus's men. There are going to take you home, and he gave me his word he wouldn't hurt you," Seto said.

     "But Seto?" Mokuba started but Seto stopped him with his finger and kneeled down again.

     "Remember you are the best little brother in the world, and they only person I trust.  I will always love you, and no matter what anyone tells you, I'm will always be with you," Seto stated.

     "Seto, what's going on?" Mokuba asked shaking not liking the idea that was going to his head.

     "I really hate to break this touching family moment, but Kaiba boy, you need to keep your side of the deal," Pegasus said alerting everyone of his presence. 

     Kimo, one of Pegasus main henchmen stood behind Mokuba.

     "Pegasus, you gave me your word Mokuba will be safe," Seto stated.

     "Of course, I'm a man of my word," Pegasus smiled.

     Seto turned to his little brother and smiled.

     "I have to go now, remember I'm always with you," Seto whispered as he hugged Mokuba.

     Everything was making sense to Mokuba now; Seto had taken his place to save him.

     Yami stay quite as the scene before him was breaking his heart; he was only doing this to save his little brother, what had he done?

     As Seto stood, Mokuba cried out.

     "No, Seto don't go, please no," Mokuba cried.

     Seto stood silent and was about to hug him for a last time, when he felt someone take hold of his wrist and pulled him away.

     "Time to go, Kaiba boy," Pegasus smiled with a card in hand.

     "No please, not in front of him," Seto stated.

     "I've been too lenient on you already, but wait.  Spirit of the Puzzle, show yourself to Kaiba boy please, I think he would like to meet you before he goes," Pegasus said in Yugi's direction.

     Yugi closed his eyes as the puzzle began to glow and everyone stepped back when a figure appeared beside Yugi, one of flesh and bone.

     "Yami," Yugi called.

     Yami had never taken physically form outside his body, not in public, not even when Tea asked.

     Yami was looking straight at Pegasus with anger filled eyes and they only softened when he turned to look at Seto.

     "It true, you're real," Seto stated, before he was consumed by a bright light.

     The next thing they saw was Seto on hid knees next to Pegasus, the only thing keeping him, from being completely on the floor was that fact the Pegasus still held his wrist.

     Pegasus let go of his hand and Seto's arm fell like dead weight.

     Yami looked into his beautiful eyes and saw that they were lifeless.

     Mokuba cried out and ran to him.

     "Seto, please wake up, please," Mokuba hugged his brother.

     "Kimo, take Mokuba back to his house, after you drop Kaiba boy's body in my bedroom," Pegasus smiled and walked away.

     Kimo was about to get him, when Yami stepped between them taking hold of both Mokuba and Seto.

     "Pegasus," Yami stated.

I hope you like it.

I haven't decided yet how many parts to the story.