A/N: I don't care how innocent and loving Yugi is, if I were him, I would've been a mess after what the Pharaoh did. That's why I've decided to rewrite the ending of the Doma Arc. Yugi expresses his pain over the Pharaoh's betrayal, and the Pharaoh will work double time to earn Yugi's trust back. This is how I think they should've handled the story, it would've added so much more depth to their bond, and let's face it, it would've been much more believable. Besides, I think a lot of us like to see the Pharaoh suffer a little because it shows how deep his love for Yugi is. He doesn't show it as much otherwise. I hope you like it, review please!

And to those who read my other story, "Broken," I'm just a little stuck on my next chapter, but I'm sure that won't last too long.

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Atonement

Chapter One

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"If you want to wipe out mankind you'll have to go through me!"

Yugi stared at the Pharaoh in horror as the evil laughter of Dartz echoed in the air.

"I'm going to enjoy this!"

The dark creature lunged at the Pharaoh, snapping its jaws to trap his soul inside. Yugi heard the Pharaoh cry out in pain, and he stepped toward the sound involuntarily. The Leviathan transformed itself into a vortex of sorts, and Yugi could see his other half screaming inside.

"No! Let him go!" Yugi ran forward to aid his friend, but the Pharaoh held up a cautionary hand.

"No, get back! This is my battle now! I must prove that the rage within me is gone!"

Yugi froze. His blood turned to ice as he remembered the Pharaoh's betrayal:

"Pharaoh, no!" Yugi cried out, doing his best to restrain his own arm.

"We must do this…now let me go!" The Pharaoh snapped, pulling his arm away in a sudden burst of rage. "Now I activate, the Seal of Orichalcos!" He slipped the card into the slot and the Seal appeared on the field. The Pharaoh cried out in surprise as the mystical energies of the Seal coursed through him, unlocking the darkness within.

"NO!" Yugi screamed, but it was too late. The Seal had separated them from one another, and the Pharaoh had given in to his inner darkness.

Yugi blinked as he tried to pull his thoughts away from that horrible memory. He looked at the Pharaoh again as he continued to explain. "When I played that card, I unlocked the evil within my heart. Ever since, I have been fighting the anger within me! And now it's destroying me!"

Yugi looked down at the floor as the Pharaoh continued to hold out against the pain. "But…you…you stopped it, didn't you?"

"No, defeating you in that duel was just the first step, I have a long way to go…"

Yugi snapped his head up to look at his partner. The Pharaoh was barely standing as the darkness continued to engulf him. The spirit grimaced and cried out yet again. "Get out of there while you still can!" Yugi screamed to him in desperation.

The Pharaoh turned to him. "No, you must trust me!"

Yugi blinked again. He stared into the face of his closest friend, his other half, and remembered. He remembered everything he had gone through. He remembered the Pharaoh's betrayal. He remembered all of the fear and suffering he and his friends had experienced throughout the recent years. He averted his eyes from his partner and took a deep breath.

"I…I can't."

The Pharaoh stared at Yugi with wide eyes. "What are you saying, Yugi?"

Yugi looked him in the eye with a newfound conviction. "Let's face it, Pharaoh! The last time you made a decision against my wishes, you lost my soul!"

The Pharaoh's jaw dropped ever so slightly and his eyes filled with tears of misery. "I…I'm sorry…"

Yugi stepped toward the vortex angrily. "That's not good enough! I don't want your apologies! I want my life back!" He dropped to his knees and stared blankly ahead. "Look at what my life has become! Instead of doing homework and falling in love, I'm out here, risking my life again and again! I'm tired of it! I just can't take it anymore!" Tears filled his eyes. "The person that matters the most to me won't even listen to my small request! You're constantly being taken away from me, why can't you just give me what I want for a change?"

The Pharaoh face twisted with pain. "Yugi, stop this!" He snarled.

Yugi looked up at him again. "No! You have made so many decisions for me, but when I ask you to do something my way, you don't listen!" He pointed at the Pharaoh. "Get out of there, now!"

The Pharaoh stared at him, dumbstruck. "I can't Yugi, this must end now!" He cried out, desperately trying to get through to his other half.

Yugi looked down at the Millennium Puzzle. He felt hot tears trickle down his cheeks as he admired the golden pendant. "You're right…this must end now…"

The Pharaoh blinked at Yugi incredulously. "What do you mean?"

Yugi glared up at him. "I have worn this Puzzle! I have kept your soul with mine, safe and sound! It has been a burden weighing down my heart! It has brought me nothing but disaster!" He wrapped his fingers around the chain. "It's over! I'm done, we're done!"

The Pharaoh reached out to him. "No, Yugi, please! Listen to reason!"

Yugi shook his head and squeezed his eyes shut. "Shut up! For once, just shut up!" He ripped the chain from his neck and tossed it away from him. He backed away from it as if it were a diseased rat. "I'm…I'm done…"

The Pharaoh dropped his arm to his side in defeat. "Yugi…"

Dartz's laughter was heard again. "Yes, Yugi…it is all the Pharaoh's fault. I can help you. Just make him feel even more of your pain, and I can erase him from existence…you can go back to school. You can be with your friends and fall in love, just like you want."

The Pharaoh shook his head desperately. "No, don't listen to him! Please!"

Yugi pretended to not even hear either of them. He stared at the Millennium Puzzle, a thousand voices screaming in his head to choose a side. It was no contest.

"Pharaoh, you are far too weak to resist the power of the Great Leviathan! Your pain and suffering over little Yugi's revelation has made sure of that!" Dartz laughed yet again. "Prepare to be erased from existence, Pharaoh! This is farewell!"

The Pharaoh closed his eyes and braced himself for the inevitable. Anything is better than Yugi's hatred…

Yugi snapped out of his stupor and grabbed the Millennium Puzzle. He threw it around his neck and lunged at the vortex in a sudden surge of rage. The Puzzle started to glow, and his hands met the Pharaoh's side in a forceful push. The Pharaoh's eyes shot open as he felt himself tumbling out of the vortex. He gaped at Yugi when he realized what had happened.

Yugi fell down on one knee. The power of the Leviathan's vortex was crippling, and he could feel his very soul being torn apart at the seams. He breathed heavily as he tried to find the strength to banish the beast, but it eluded him. He shut his eyes tightly as he fought against the pain, but it was unbearable. He screamed in agony as the darkness clawed at his heart.

He could barely hear the Pharaoh's desperate cries over his own fading heartbeat. It thundered in his ears as he realized that he had finally pushed the envelope. He had known that there was no way he could survive so much without a scratch, but he never expected that his own blind loyalty to the Pharaoh and mankind would be his downfall. Tears slipped past his eyelids as he felt the darkness swallowing him whole. It was cold and persistent as it wormed its way through Yugi's heart and mind. His whole body felt like ice and he began to shiver.

"You young fool! Your rage at the Pharaoh only fuels the Great Leviathan! You cannot even hope to survive, and once you're out of the way, it will make short work of the Pharaoh as well!" Dartz yelled out confidently.

The Pharaoh felt absolutely helpless as he watched his partner being consumed by the Leviathan. He knew he had to do something, but he had no idea what. He turned his face away from the scene and squeezed his eyes shut. He had never felt such tremendous pain.

"No matter what, as long as we're together, we can face any evil that comes our way!"

The Pharaoh opened his eyes. Yugi had said those words to him before, and in his heart, he knew them to be true. He needed to be with his other half, even if it was just to face their inevitable demise. As long as they were together, that was all that mattered.

The Pharaoh ran toward the vortex but Yugi glowered at him. "Stay back! Don't come near me!" He screamed, his voice faltering from the pain he was experiencing.

The Pharaoh stared deep into Yugi's eyes and continued to move toward him. Despite the livid expression on his partner's face, he knew that if they had any chance at all, they had to be together. He stepped into the vortex, immediately feeling the overwhelming force of the Great Beast. He used all of his strength to reach Yugi's side, and he squatted next to him. His eyes bore deeply into those of his other half as he spoke: "No matter what happens, we're in this together."

Yugi shook his head vehemently. "We're done!"

The Pharaoh clenched his jaw and spoke through gritted teeth. "I don't care what you say, Yugi, you can't survive this alone!" He scolded fiercely.

Yugi looked away from the Pharaoh. He could feel himself slipping away, and he knew that he didn't have much time left. He yelped as he suffocated in his own rage. He swallowed hard and tried to let go, but it was too difficult. The Pharaoh's betrayal had cut deeper trenches in his heart than he had previously thought.

The spirit grabbed Yugi's hand. The boy looked at him, his eyes barely open as the Leviathan continued to devour him. The spirit cringed at the sight, but he swallowed his heartache and tried to be strong. "Yugi…"

Yugi's eyes fluttered, and the effort to keep himself grounded was too much for him. He furrowed his brow as he spoke to his other half. "This is all…my fault…"

The Pharaoh gasped as Yugi fell to the ground lifelessly. He screamed in agony at the sight, and he felt a new fire burning in his heart. He closed his eyes and took control of the shell Yugi had left behind. He stood with new determination.

"That was your fatal mistake, Dartz!"

He glared up into the vortex he was now alone in. "You forgot about one thing! The Great Beast was beaten back once before by the light in peoples' souls, and now that it is but a shadow of what it once was, I can do that again!"

Dartz dismissed this. "Don't be ridiculous, Pharaoh! There isn't a shred of light in your soul, especially now that your other half is about to become one with the Great Leviathan!"

The Pharaoh smirked. "There is one glimmer of hope in my heart, Dartz! The light that Yugi left behind still burns within me like a powerful inferno! It's love." He swallowed against the lump that had formed in his throat as he placed a hand over his heart. "My love for Yugi knows no bounds!"

He closed his eyes and a faint golden glow covered his entire body. He suddenly felt safe, and no pain penetrated the light. He smiled fondly. "This is for Yugi," he whispered. The strength and determination returned to his face as he spread his arms far apart as if he wished to embrace the vortex. "With all of the light in my heart, I banish thee! Be gone!"

The golden light that emanated from the Pharaoh expanded, engulfing the darkness and blinding everyone. The spirit squinted through the light, trying to determine whether or not he had been successful. When he heard Dartz scream in shock and anguish, he breathed a sigh of relief.

The light soon vanished, and the Pharaoh's ability to see returned. When it cleared, the darkness was gone as well. The Pharaoh frowned as he looked down at the Puzzle. "But…Yugi…"

"He never left you."

The Pharaoh looked up in surprise. Ironheart stood next to the unconscious form of Dartz with his granddaughter, Chris.

"The Great Leviathan hadn't succeeded in taking his soul yet, you had perfect timing. If you had waited any longer, your little friend's soul would've been destroyed," Chris explained, beaming at the Pharaoh. She kneeled next to Dartz. "Wake up, father! We have a lot of catching up to do!"

The Pharaoh took a wary step back as Dartz opened his eyes and slowly pulled himself off the ground. Chris threw her arms around him and he smiled. He turned to the Pharaoh, his smile replaced by a grim expression.

"I will forever be in your debt, Pharaoh. I…I apologize for everything I have done…"

The Pharaoh held up a hand to keep him from saying anything else. "I fully understand what it is like for your inner darkness to take control of you. Don't apologize…there is no need for it."

Dartz gave him a small smile. "Thank you. I do hope we meet again."

The Pharaoh gave him a thumbs up gesture. "Likewise."

Ironheart pointed to the portal behind the Pharaoh. "It's time for you to return to your world. Take care, Pharaoh, great things await you."

The Pharaoh smiled. "Thank you, for everything."

He turned around to walk out of the portal. He hesitated as he felt Yugi's soul stabilizing inside of him. Cold dread gripped at his heart as he thought of the hatred Yugi harbored toward him. He prayed silently that Yugi's anger had dissipated.

He pressed on and entered the portal. As he felt himself being pulled through, he suddenly lost consciousness.

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Yugi opened his eyes slowly. He recognized the sound of crashing waves and inferred that he had washed up on a beach somewhere. The question, however, wasn't where he was: it was how he got there.

He pulled himself up and turned around to look out over the ocean. The sun was beginning to set on the horizon, casting an orange glow on the landscape. He breathed in deeply as the memories of his confrontation with the Pharaoh returned to him. He clenched his hands into fists as he recalled every word he had said to his other half. That's when a thought struck him. He frowned in confusion. "What happened?" He thought aloud.

"We won."

Yugi gritted his teeth at the sound of that voice. "You won."

The Pharaoh walked in front of him and turned to face him. He searched Yugi's eyes, desperately trying to find a shred of the love they had once shared. His heart shattered into a million pieces as he realized that love was very much one sided at the moment.

"I couldn't have done it without your light, Yugi," he said quietly.

Yugi turned his face away from his partner. "It's my fault that it even happened in the first place."

The Pharaoh shook his head. "Don't be ridiculous, it was no one's fault."

Yugi nodded slowly. "Yes it was. I completed the Millennium Puzzle. I unleashed the power of the Shadows on the earth. I gave Dartz the opportunity he needed to resurrect the Great Leviathan." He looked back into the Pharaoh's eyes. "I set you free."

The Pharaoh felt cold after hearing Yugi's cruel words. "You don't mean that…"

Yugi lurched forward angrily. "You can't tell me what I mean and what I don't! Face it! The world would've been better off if you had never come back!"

The spirit gawked at Yugi. "Where is this coming from? You seemed fine until I asked you to trust me."

Yugi nodded. "That's just it, you made me realize that I don't trust you."

The spirit turned his back on Yugi. He gazed out over the ocean with pain in his heart. "Please…just tell me what I can do to make it up to you…"

Yugi laughed. "It's not that simple! You can't take back what you did, and you can't just make it all go away! The fact is, you betrayed me Pharaoh, and that opened my eyes to what you really are!"

The spirit whirled around to glare at him. "And what am I, Yugi?" He growled.

Yugi dug his fingernails into his palms and bit his bottom lip as he fought to contain his anger. "You're a liar!"

The Pharaoh blinked in surprise. He stared at Yugi with a passive expression on his face. "I have never lied to you, Yugi."

Yugi looked away, his eyes glistening with new tears. "You always said that we were partners. You convinced me that we would work together, no matter what happened. I thought we were a team…" He sighed and began to shake. "I was wrong."

The Pharaoh took a step toward him, but he backed away. "Yugi, please…we are partners. We have a bond that no one could break, not even with a thousand swords. I made one mistake, please…" The spirit dropped to his hands and knees. He stared at the sand as tears blurred his vision. "I'm begging for your forgiveness…"

Yugi removed the Millennium Puzzle from around his neck and looked at it. "I don't want that bond…not anymore," he whispered between tears. He ground his teeth together as he glared at the object. "I want to be alone."

The Pharaoh looked up at him. "You'll never be alone."

Yugi shook his head. He heard the sound of a helicopter landing on the other side of the beach. He heard the faint cries of his friends as they raced toward him. An overwhelming calm overtook him as he realized what he had to do.

"I know a way to break that bond."

The Pharaoh jumped to his feet and caught Yugi by the shoulders. "Yugi, NO! Don't do it!" He screamed desperately.

Yugi swallowed hard and ignored his other half. He shrugged off the Pharaoh's hands and turned around. He kneeled beside a rock and raised the Puzzle high above his head. He felt the spirit's fingers wrap around the object in a vain attempt to keep him from completing his task.

"Please, Yugi! I will do anything, just don't go through with this!"

Yugi squeezed his eyes shut and screamed. "Shut up! Just leave me alone!" He brought the Puzzle down on the rock with surprising force. He felt the many pieces crumble in his hands as it came into contact with the hard surface. Without opening his eyes, he leaned forward and rested his head on the rock. He sobbed uncontrollably as his friends watched him in shock.

Joey, Tristan and Téa could hardly believe what they were seeing. They had never seen Yugi filled with so much anger and at the Pharaoh no less.

They watched their small friend in silence as they all tried to guess what had happened. They couldn't imagine something coming between Yugi and the Pharaoh. Their link was so strong that it had survived a lot over the years.

After a while, Yugi raised his head and slowly began to gather the pieces of the Puzzle. He knew deep down that he would eventually put it back together and face his other half, but in that moment it seemed out of the question. Joey kneeled beside his friend and started to pick up pieces as well. The pair didn't say a word to each other as they worked. Lastly, Joey picked up the chain and put it around his own neck for safekeeping. When they finished, they stood up and walked toward the others.

Tristan held out his hands to Yugi. "I can…take those if you would like," he offered, nodding his head in the direction of the pieces. Yugi gave him a small, grateful smile as he dumped the pieces into his friend's hands.

Téa placed her hands on Yugi's shoulders in an attempt to comfort him. She sighed sadly. Even though she had strong feelings for the Pharaoh, her loyalty to her best friend surpassed that. "I'm really glad that you're okay, Yugi…"

Yugi nodded absent-mindedly. "Thanks Téa…" his voice cracked from the many tears he had cried.

Téa winced at the sound of his weak voice. She gave Yugi a small nudge in the direction of the helicopter. "We better get out of here before Kaiba decides to take off without us."

Yugi gave an awkward laugh. "Yeah, I'm sure his urge to help us is wearing off."

Joey scratched his head and laughed half-heartedly. "Yeah…that's good ol' money bags for ya…"

The four of them walked in silence to the vehicle. Yugi noticed Mokuba and Seto standing in the doorway of the helicopter, watching him carefully. Yugi sighed. They saw…he thought sadly. He braced himself for Seto's sarcastic remarks, but they never came. He passed the young CEO and stepped inside, and not one word was said.

Kaiba followed Yugi inside and sat down. He watched Joey and Tristan carry in the remnants of the Puzzle with a troubled heart. I've never seen Yugi act like that before…he thought, seeing someone as friendly and kind-hearted as him lash out so aggressively is unsettling to say the least.

As the helicopter took off from the island, Yugi stared out of the window. His friends didn't try to disturb him, for they were all still slightly afraid of his anger. They had no way of knowing that his rage had been replaced by a painful emptiness. Even though he was furious with his other half, he couldn't help but feel incomplete without their connection. He didn't let that influence his actions, though. He wasn't ready to forgive the Pharaoh, and he wasn't sure how long it would take for that time to come.