Still don't own Naruto

Chapter 65: The Origins of Pein

Naruto arrived at a huge tree and stopped to make sure he was in the right place. 'It's here he must be inside this tree' Naruto thought as we placed a hand on the tree and felt it buckle slightly. 'It's made of paper, this must be the work of Konan. Jiraiya sensei told me she uses origami jutsu'

Naruto pulled his hand through the tree and ripped apart an opening. Stepping inside Naruto came to a halt, sitting in a large machine with chakra rods sticking out of his back and looking like he had wasted away was a man with red hair and Rinnegan eyes.

"Nagato?" Naruto asked his anger at the man momentarily ebbed away at seeing one of the most powerful people ever to live looking like he was on his death bed.

"So you have arrived" Nagato said slowly raising his head to look at Naruto properly.

Konan who was standing to the side of Nagato moved in between the two Uzumaki "You will not get anywhere near him" she said shielding Nagato from any possible attack from Naruto.

"Konan enough, move out of the way, there is no need for you to get involved" Nagato said calmly.

'Interesting, he obviously still cares about some things' Naruto thought as Konan moved off to the side.

Naruto slowly walked into the tree that Konan had created. Nagato saw Naruto's guard was down just slightly and sent a chakra rod soaring from his machine and impaling Naruto.

The blond didn't move however as he saw the sharp metal approaching him, he knew he could avoid it but still allowed the rod to hit him in a non vital area.

Naruto could feel Nagato's chakra inside of him trying to influence him but he knew how to cancel the effect out. Naruto channeled a small amount of Kyuubi's chakra into his system.

Nagato obviously felt the surge of demonic chakra as he was forced to remove his chakra rod. 'He let himself be hit, why?' the red haired Uzumaki thought as he narrowed his eyes at Naruto.

"I came here because I wanted to meet you, when I was training with Jiraiya sensei he always spoke so fondly of you. Then I found out you were the leader of the Akatsuki and almost killed Jiraiya sensei. I wanted to know how someone who was trained by my own teacher could have turned out like you, you say that you're doing this all for peace, your peace is nothing but an illusion" Naruto said his eyes that were glaring at Nagato were a mixture between the slit like pupils of the Kyuubi and the Bar like Sage Mode eyes.

"You want to know about my pain? Why? That would not accomplish anything. And what do you know of peace, can you honestly tell me you know of another way to bring ever lasting peace?" Nagato said.

"Off the top of my head, no. But our sensei believes that there will be a time where people would truly be able understand one another and that would bring peace to the world. I may not have all the answers yet but as Jiraiya sensei's pupil I believe in him and his dream of a real peace" Naruto said.

"Childish dream's of our foolish sensei, do you really think that would work?" Nagato asked.

"I don't know, but I refuse to give up, Answers to life's important questions are not supposed to come easy, just because your way seems the easiest does not make it the right one. I came here to confront you, but also I wanted to see what I would do standing in front of you" Naruto said.

"And what have you found?" Nagato queried.

"I hate you, you have caused so much pain I want to kill you so badly it almost hurts. But I also piety you. there has obviously been things that you have seen that turned you the way you are today" Naruto said still glaring at Nagato.

"I see" Nagato replied.

"Yes I want to kill you... But I will not do it, you said yourself, there is a circle of hatred in this world. I plan on ending it. And I am going to start with you, you have been consumed by your pain and sorrow until this is what you have become I understand that" Naruto said his face calming slightly before continuing.

"You claim to understand my pain, that is not possible. Nobody can understand the pain that I have felt" Nagato said disbelievingly. His eyes had widened at Naruto's proclamation that he would not kill Nagato, no matter how much he wanted to.

"That's not true, there are at least three people who have felt the exact same pain, sorrow and helplessness that you have felt. But before I tell you more, I would like to hear your story. I want to know how you turned out this way" Naruto said.

"You want to hear about my pain? Very well. I will tell you" Nagato said. His observations of the boy told him that he was not lying and he truly believed he knew his pain, he was also sure the boy had some information that the blond had not shared yet.

"Thank you" Naruto said, his eyes returning to there Azure blue as his Sage Mode faded and he had long ago stopped channeling Kyuubi's chakra.

"Nagato, this is a waste of time, lets just finish him now" Konan said.

"No it can wait Konan, I want to here what he has to say. Besides, it will not be easy to take him down. I cannot move freely as you know and he can move where ever he wishes in under a second, with the Hirashin. He was able to defeat all six of my bodies and make it here all by himself" Nagato said calmly.

"Very well, if you think that this is important, then I guess I can wait" Konan said.

"There are two incidences that fuel my pain" Nagato said beginning his story, but before he could continue Naruto cut him off.

"The first awakened your Rinnegan and the second led to the creation of the six path's" Naruto said knowingly.

Both Konan and Nagato's eye's went as wide as saucers at Naruto's knowledge. "Yes, but it is amazing that you could know that" Nagato said in disbelief.

"I will tell you how I know once you finish with your story" Naruto informed the pair.

"Very well I will begin with my first great pain, the loss of my parents. It happened when Ame got dragged into the war between the great shinobi nations. My family lived in a small village well outside of Ame but one day a group of Konoha shinobi broke into the house looking for something to eat. My parents and I were hiding, as far as I know the ninja from Konoha did not know we were there. After awhile my parents suggested we make a run for it. On the way out I accidentally bumped a small table and knocked over a bowl which shattered on the floor alerting the ninja to our presence, father tried to buy my mother and myself some time to escape and charged. This however just made the ninja think it was the enemy attacking. They killed both of my parents before my eyes. I vaguely remember the Konoha shinobi repenting what they had done once they realized my family were nothing but civilians. Then one of them came over and began to apologize but it was too late my sorrow was consuming me. The last thing I remember was a huge burst of a need to do something to no longer be helpless" Nagato said.

"And when you awoke the men who had killed your parents were dead and you had awoken the Rinnegan" Naruto said sadly, his hatred towards Nagato was slowly fading, he had experienced a similar feeling and pain when he thought there was nothing that could be done to save Jiraiya, and he would not wish that feeling onto anyone.

"Yes. Both my mother and father were killed in that war that your village, Konoha, started. I never let go of the pain I felt then, I carry it with me even now. That pain manifested into hatred, and gave rise to my power" Nagato said.

"It was not your hatred that gave you power. It was the sorrow and loss of someone you loved so dearly you would do anything to get them back. A power that the Rinnegan has I believe. It was your love for your family and the need to protect and save them when you were completely helpless that gave you your power." Naruto said exhibiting more of his knowledge of the Rinnegan.

"Yet again you demonstrate more knowledge than anyone else ever has on my abilities, but this is the first time anyone has suggested it was a need to protect that activated my Rinnegan" Nagato said, subtly contemplating Naruto's words.

"I promise I will tell you everything I know but first please continue your story" Naruto said.

"Very well. After I buried my parents I was forced to leave home, there was no food there anymore. I continued to travel, begging for food, until I had completely given up. That was when Konan found me and took me to where she lived and I met the boy named Yahiko. They were also orphans of war, but they were strong and fought for their survival. And I became there friend. They taught me to survive by taking what we needed. As children with no families and no organizations to help us, we had no choice. However even faced with the darkness of reality Yahiko never gave up" Nagato said with a small smile remembering his old friend.

"Sounds like he was quite a good friend" Naruto said.

"He was. Anyway continuing on. Towards the end of the war we were walking on to a new town when an explosive tagged kunai landed in front of us, we were lucky and uninjured but there were more explosions going off, when we made it to the top of a cliff we overlooked a battle, the fight was between the old ruler or Ame, Hanzo the Salamander, and three ninja from Konoha. It was Jiraiya sensei and his two comrades. The three would later be known as the Sannin of Konoha. We fled the fight for safety and went and hid in a cave. That was when Yahiko told me about his dream. To stop the fighting he would become the ruler of the world if he needed to. And that was when Yahiko's dream became my dream also. Later that night Yahiko told us that if we really wanted to change Ame for the better we would need to become powerful, and that we would have to learn ninjutsu" Pein said.

"So you hunted down Jiraiya sensei" Naruto guessed.

"Indeed. We figured if they were able to take on Hanzo and live then they must have been amazing ninja. I was rather hesitant to go after them, after all they were Konoha shinobi and it had been Konoha who had killed my parents. But I agreed after seeing how strong Yahiko's conviction was. We packed bags of food that would last and set out in search of the three Konoha ninja who had survived a battle with Hanzo. But pursuing the sannin was quite a challenge. In order to follow ninja we would have to go through the war zone, as mere children. Ninja would never leave there tracks behind. Still Yahiko never gave up. One day we arrived in the center of a battle field, it was a mistake and we were almost killed, but luckily our gamble paid off. We found Konoha's sannin. We had finally found Jiraiya sensei" Naruto uncontrollably clenched his fist it this part in Nagato's story. He may have been trying to understand why Nagato turned out the way he did but was still having a hard time trying to forgive him for trying to kill Jiraiya and turning Konoha into mostly a large pile of rubble.

"Despite our good fortune of finding the sannin I still could not fully accept Konoha ninja. I'm sure you would understand why" Nagato said. Naruto simply gave a small sad nod.

"We followed the sannin as they were leaving a village and confronted them. Konan offered them one of her origami flowers. Thing's did not look good for us when Orochimaru decided that it would be better for us if we were dead. But Jiraiya sensei stopped him and offered to train us. I hated Konoha ninja, but Jiraiya sensei seemed different than the ones that killed my parents. The four of us started living together. But soon after a certain incident occurred" Nagato said.

"Incident?" Naruto queried.

"A lingering Iwa ninja attacked us and nearly killed Yahiko. That was when I struck out and killed that ninja instead. I did it without realizing it. It seemed I had a special power. That was when Jiraiya sensei first saw my eyes. And informed me that it was the Dojutsu known as the Rinnegan, the eyes of the Rikudou Sennin. After that Jiraiya sensei, who had been a little hesitant at training us, began to teach us ninjutsu. He said he was teaching us so we could protect ourselves. But I think in my case it was so I could control the power of my Rinnegan. However I was afraid of the power. Hate had caused me to go berserk. I was consumed with guilt for killing that man. But sensei pulled me from the depths of despair. He told me I did what I did to protect a friend. And that nobody could blame me for that. That was when I truly accepted sensei. He told me that when you are hurt you learn to hate. And when you hurt someone else you are resented. However if you can understand such pain it enables you to be kind to others. Knowing pain helps us to grow and to mature. And to come to there own answer for dealing with pain. Jiraiya sensei seemed to be asking himself the same question even before he left us. And he hadn't found an answer. Just like you haven't. Back then I was able to come up with an answer right away. I said 'I just want to protect Yahiko and Konan, no matter what pain I have to endure' Jiraiya sensei went on to tell me about his dream of a world without war. Three years past and I became stronger. However Jiraiya's words that day kept coming back to me sensei said that perhaps the answer rested within my Rinnegan as they were the eyes of the sage, the first person to bring about peace" Nagato said.

"Yes it's true he believed you were the child of destiny that would bring about a great change to the world. But after seeing what you have become he changed his mind" Naruto said.

"He said that he thought I was the reincarnation of the Rikudou Sennin and that I would be the one to bring peace. Sensei entrusted us with the quest for peace and then left us by ourselves" Nagato said.

"Yet rather than peace and stability you chose destruction, your family would be ashamed" Naruto said.

Nagato chose to ignore Naruto's statement and continue on with his story. "With Yahiko as our leader we created an organization and we quickly gained fame. People believed in our goal to build peace without the use of force. But the world was at war, Hanzo had heard about our organization and approached us. We couldn't be ignored anymore. He wanted to use us to negotiate peace with the three great nations who where currently at war. Konoha, Suna and Iwa. We agreed to cooperate with his proposal. But that was the beginning of our problems, we were nothing but naive children" Nagato said.

"Problems? What happened?" Naruto queried.

"Because of that Yahiko died. It was all a trap laid by Hanzo. He suspected we would try and steal his power over Ame from him. The next day after the meeting we went to the meeting place and Hanzo's troops and the Konoha Anbu were already there. Hanzo had schemed with a man named Danzo from Konoha. To help get rid of us and to usurp the seat of Hokage for himself" Nagato said a hint of sadness in his voice.

Naruto released a small blast of killing intent at this. "Danzo huh, that old bastard is always trying something, all he cares about is his own power" Naruto said before spitting on the floor in disgust.

Nagato and Konan gave Naruto a curious look, they did not suspect Naruto to react like that. "It appears that Danzo is no friend of yours either" Nagato said.

"You could say that. He runs his own branch of Anbu that work outside of the Hokage. He also has some pull with the village elders, a lot of the crimes that have been committed by Konoha have been because of that man. He only thinks of his own well being and always has his men try and follow me. He thinks I don't know about it but I can sense any life form and chakra signature" Naruto said.

"I see. Anyway when we arrived they took Konan hostage and ordered me to kill Yahiko. Konan told me to forget about her and escape with Yahiko. But Yahiko wouldn't allow it he asked me to kill him. I didn't know what to do but I picked up the kunai I was told to kill Yahiko with. Before I could even think Yahiko threw himself onto the kunai. That was when Pein was born. Typically Hanzo did not let us leave like he said he would. We were attacked by both Hanzo's troops and Konoha Anbu. I don't know how or why but an impulse came over me and I summoned a massive creature, The Demonic Outer Path, the Gedo Mezo" upon hearing the name Naruto's eyes went wide. It was the forbidden jutsu that had no information in all of the books Naruto had time to read while he was training to fight Pein.

"Is that how you ended up in that machine?" Naruto asked.

"Indeed. It was a terrifyingly powerful jutsu, with one touch of the jutsu it created it would remove the souls of anyone it came in contact with. But Hanzo managed to escape. Yahiko died and I took over as the leader of our organization. I thought I had grown up. But nothing had changed at all. Just like the time my parents had died. I realized the answer I had come up with to Jiraiya's question was nothing by crap, I owed Yahiko my life. He was my dream. He was an irreplaceable friend and brother who I would have gladly died for. Yahiko's death was my second pain" Nagato said.

"I see, so I guess I owe you some answers but first I have a story for you. Jiraiya's question was not a new one. In fact it is as old as the Rikudou Sennin. There were once two sons of a great man. He asked them both on his death bed how they would achieve peace. The elder brother believed peace could be achieved through strength of might, and military force. Much like yourself. The younger brother however disagreed and said true peace come not from conquest but understanding and kindness. There father after listening to how there sons answered the question named his younger son as his heir before he died as his path was the one he would have chosen. These two sons were names Uchiha and Senju. And there father was Ryuga Uzumaki, the Rikudou Sennin" Naruto said shocking everyone listening including Katsuyu who had been forgotten hiding inside Naruto's cloak.

"Uzumaki? You called me that back in Ame, I have no family how could you know something like that" Nagato asked in shock.

"It's simple really, the Rinnegan is our bloodline, only an Uzumaki can awaken the Rinnegan. As to how I know, well the answers are here" Naruto said taking out a scroll and unsealing the large book that became a Diary. Flipping to the first mention of the Rinnegan and the Rikudou Sennin he handed the book over to Konan who began to read her eyes widening with each line that she came to about the sage.

"This is unbelievable, here Nagato look" She said and she passed the book up to Nagato who lifted a hand out from one of his large gauntlets that kept him in place to accept the book.

"Where did you find this" Nagato stammered in disbelief.

"Uzu, where your mother was from. There is an active bloodline family tree jutsu in Uzu that traces our family right back before the Rikudou Sennin to when that book was first written. You are in fact the fourth wielder of the Rinnegan" Naruto informed him.

Nagato continued to read on flipping to the next page while Naruto continued his lecture. "These people understood your pain, but it was not hatred that made them strong, it was unimaginable sorrow and helplessness. The kind of sorrow you get from loosing someone you love right in front of your eyes while there is nothing you can do to stop it or save them. In fact I felt the start of the transformation myself but my body has a fail safe with a mind of its own. I suggest you read the parts on Meto Uzumaki, she was the first one to feel the same pain twice, just like you did, after that she created her own six paths, but rather them be her paths of pain as you called them, she called them her paths of sorrow" Naruto said.

"To think there have been others like myself" Nagato said.

"Yes there are, you had a family, the Uzumaki clan never wanted any violence, that is why they kept the Rinnegan a secret. They lived on a small island where they accepted almost anyone. They had peace. The Rinnegan is a mark of sadness inside our clan, and the people who wielded them were to be honored. You asked me how I would achieve peace earlier, the same question was asked to me by Jiraiya sensei just like he asked it to you all those years ago. I still don't have a proper answer, like Jiraiya sensei and Senju before him I believe in a time where people will be able to truly understand each other, without the need to conquer the world or make the people live in fear. It is not a question with an easy answer, if it was we would have peace already, or maybe it's because so many people have come up with your answer that we have so many wars. You may be right. Maybe true peace is impossible, I can understand where you are coming from. But Jiraiya sensei believes in me and in his quest for true peace. So his beliefs will be my own" Naruto said.

"I see so you will believe in Jiraiya sensei's fool of a dream. And what do you expect us to wait until you make this world a peaceful place? Impossible, there is no suck thing as true peace in this cursed world, its impossible" Nagato said.

"Then... I guess I will have to break that curse. If there is such a thing as peace I will seize it! I'll never give up" Naruto said loudly hoping Nagato would recognize them.

"That's... Those words" Nagato said once more.

"That's right, they came from this, Jiraiya's first book" Naruto pulled a small green book from inside his kunai pouch. "Jiraiya sensei was seriously trying to save the world with this novel. At the end of the book he wrote about a student of his who provided him with the inspiration to be a writer and to try his own way of bringing about peace. You were his inspiration, Nagato" Naruto said.

"I... I spoke those words to sensei, but there was more, I needed the power to believe in it... I lost that power ago. He left me a copy of that book. The hero who would never give up no matter what his name was... it was" Nagato tried to remember the hero's name but it was slipping his mind. Suddenly realization sunk in and he remembered. 'It was him, his name. Naruto!... You are the savior of this world, not me. You believe in peace and work towards it, all I have done is cut corners. Sensei once told me about a prophecy that one of his students would change the world, he believed in me and I failed him. But you, your different. You will save this world' Nagato thought his eyes widening.

"His name is Naruto. My parents named me after the ninja in Jiraiya sensei's book my name is a precious keepsake from him I cannot give up, I refuse too. It would shame sensei's gift to me. I will be the one to establish peace and order, like the Ryuga Uzumaki before me" the blond said.

"How... how do you know, that you will not change no matter what pain you face or how great it is. Can you continue believing in yourself then?" Nagato asked.

"I have experienced pain too... as a child I was alone, I had no friends no family. I was even beaten sometimes by drunks, but mostly just ignored and hated. I was lonely and like you my pain was beginning to consume me, but I was saved. One man believed in me, and then I met jiriaya sensei and traveled and trained with him. And slowly people began to give me some attention and acknowledge me for things other than being the Kyuubi jinchuuriki. Then when you almost killed sensei my world collapsed around me and I felt the pain and sorrow you must have felt when your parents were killed. I hated you, I wanted to go back to Ame and turn the village into nothing more than a memory in revenge. But I couldn't do it, I was angry at you and revenge is never the option, innocent people would be hurt and that is not our sensei's way, its not my way. If I stop believing in myself because of some more pain. Then I will no longer be Naruto. I can't write novels the way sensei does and all of his are mostly smut now so the sequel will have to come via the life I live. No matter what pain I have to endure I will continue on my path. Because that's who Naruto is. And that is who I am" Naruto said confidently.

"If the hero changes, the story will be different... you and I are so much alike, we are sibling disciples from the Uzumaki clan. As students of the same master we should be able to understand one another, you remind me of how I once was, but I lost my power to believe in peace, I wasn't able to believe in Jiraiya. Nor could I believe in myself. However you walk towards a different future. I will believe in you, Naruto" Pein said before forming a hand seal. "Outer path: Samsara of Heavenly Rebirth"

"Nagato! Don't!" Konan shouted once she figured out what he was planing.

"Enough Konan I am making a new decision. A decision I had once given up on" Nagato said his voice filled with determination.

"What are you doing? the Samsara of heavenly life brings souls back to life, who are you reviving?" Naruto asked.

'If he performs that jutsu now with his chakra levels so low he will die, is Nagato really prepared to sacrifice himself for this child? He managed to change Nagato this much how is that possible?' Konan asked herself.

(Konoha)

In the center of the nearly completely destroyed village a large statue began to rise from the ground.

"What is that thing?" Tsunade asked and she began to grow scared at the sight o the statues Rinnegan eyes.

The statue began to spew hundreds of green beams all over the village that made Konoha glow.

Slowly the beams of light made there way to bodies of the diciest members of Konoha and slowly they started coming back to life.

(Myobokuzan)

"It is done" The elder toad sage said from where he sat with his crystal ball.

"It is? What happened?" Jiraiya asked with Yugito struggling not to throttle the old toad for not giving her regular updates on Naruto's condition and how he was doing in the fight.

"It is as I prophesied, but there are two children of destiny, them meeting was fated and once they came together there goals became one. But it seems that this is the end for the elder apprentice. He is giving his life to believe in the blond one oh what's his name again?" the elder sage said once aging showing his old age.

"So Naruto is safe?" Yugito demanded questioningly.

"Ah yes that is it, Naruto. Yes the boy is safe. And thanks to his words he has brought the villagers back to life" the sage said getting a sigh of relief from both Yugito and Jiraiya.

'So Naruto saved Nagato from himself, I am so proud of you kid' Jiraiya thought as a smile began to cross his face.

(With Naruto)

Naruto began to grow concerned when Nagato's blood red hair began to change to white. "He Nagato what are you doing? if you keep that up you're going to die" Naruto said.

"It's alright, think of it as a parting gift to you, you gave me the family I never knew and saved me from myself. This is the least that I can do for you. I am bringing everyone back to life that was killed today by me or by Konan" Nagato said.

"You can't it will kill you" Naruto said urgently.

"That is alright, there is no place in the peaceful world you and sensei dream of for me. I lost my right to live there, you will bring peace to this world Naruto... I believe in you" Nagato said as his hair finished changing to pure white.

"You still wanted peace, your way of acquiring it may have been misguided but you genuinely believed in creating a peaceful world, you deserve peace more than anyone" Naruto said.

"It's too late for me, but I can die happy knowing Yahiko's and my own dreams are alive within you" Nagato said with a smile.

(Konoha)

People all over the village were waking up, in the hospital the body bags that had been filled were being torn open and people were flying out of the morgue.

"Impossible, what is happening?" Sakura asked as more and more people she had checked herself had awoken from death.

"It is because of Naruto. Pein is returning everyone that was killed in the village back to life, he has chosen to believe in Naruto" Katsuyu said.

That was the message Katsuyu was relaying all across the village.

"So Naruto won? Alright, he did it" Kiba yelled when he heard the news"

"Actually they didn't fight, they just talked but somehow Naruto was able to convince Pein of the error of his ways and to repent Pein is returning the lives that he stole" Katsuyu informed the group.

"Yosh! Naruto's flame's of youth just keep burning brighter and brighter" Lee said in his typical over enthusiastic manner.

"You're right Lee, we will have to begin to train even harder is we want to keep up with him" Gai said causing Neji and Tenten to pale slightly at the thought of how bad it was going to be to train with Lee and Gai for the next couple of weeks at least.

Tsunade was checking on all of the people who had begun to be brought back to life. 'There, completely healthy, I don't know what you did kid but you have saved the village' she thought as she looked around to see more and more people waking up.

Kakashi and Asuma awoke at the same time and sat up. They immediately went to check on there wounds but there were non. "What the hell is going on here? I was certainly dead, I talked to my father" Kakashi said completely in shock.

"I remember being stabbed then nothing, I don't get it what's going on?" Asuma asked nobody in particular.

Luckily for them a Katsuyu clone stayed close by and informed them on the outcome of Naruto's battle with Pein. "He did it huh, well if anyone could it would have been him" Kakashi said proudly.

"Come on let's go back to the village" Asuma suggested.

"No you go, I think I will go escort Naruto back home safely, in case he is tired" Kakashi replied.

Outside the village Zetsu sat watching the events before him. "Oh Madara is not going to like this" the black half said.

"We need to go inform him at once" the white half replied before they sunk back into the tree they were standing on.

End Chapter!

Pein Arc basically done, time for an original Arc before the five Kage summit, I have a vague idea of what I want to do but I may need a couple of days to figure it out so update after next chapter may not be right away like others have been, sorry.

Anyway hope you like it. I will be add a little bit more of Nagato's reaction to being an Uzumaki next chapter. Hope you don't think I made Naruto forgive Nagato too easily, I mean he was able to forgive him in the cannon and he had killed Jiraiya. This time he had a small idea of some of the things Nagato would have had to of been through in his life prior to meeting him, and Jiraiya was still alive.