Naruto didn't know what to make of the main Pain's power. It was so weird. "What the fuck was that?" Naruto asks under his breath. Then, he walks up to the Pain he was facing and lands a finishing blow to his skull, cracking it open under the pressure of his fist. That Pain had not been able to stand after Naruto punched him before the main Pain dispatched Naruto's shadow clones. Naruto looks over the remaining opponents. The Pain that could summon, bring back the dead, and the one that absorbs Ninjutsu were killed. So the ones remaining were the main Pain, a baldie with a dopey smile and one with long hair and a neutral expression on his face. Naruto didn't know the abilities of any of the Pains remaining. Except for main Pain, who could do some weird pushing jutsu. Naruto reasoned that the others must have some bizarre jutsu as well.
Naruto sinks down into a defensive taijutsu stance. He wouldn't run into battle unprepared. "Katsuyu..." Naruto says loud enough for the slug to hear him. She pops up from his flak jacket. "Yes, Naruto-sama?" She asks. "I am going to need you to look out for any patterns to the remaining Pains. This, from now in is a blind, three on one fight. It doesn't seem like I can summon any clones to even out the score either," Naruto lays out the situation. "Hai! I'll look out for anything you can use," Katsuyu says. "Thank you," Naruto says, closes his eyes and takes a deep breath to refocus on what he has to do. He opens his eyes and zero's in on the closest Pain. He reexamines the area for any Hirashin kunai he can take advantage of. He doesn't find one, so he produces a few more from his pouch. He throws them out, but it seems like the Pains have learned from their previous bout, he lifts his hand and pushes them out of the air before they can land, and they land behind Naruto. "So I won't be able to use Hirashin against him... That is annoying..." Naruto says to himself. "It is useless..." Pain says. "You should give up now. The more clones you kill, the stronger the ones remaining will become. The peace Jiraya-sensei talked about will finally be realised with your death," He adds. "Jiraiya-sensei..?," Naruto asks. "That's right. I was Jiraiya's student before you. I have lived in his teachings and found them thoroughly lacking. That is why need you to be sacrificed so the world will finally have peace, even if it will only be for a little while," Pain says. "I see..." Naruto seemingly gives up. "I will give you one more chance: Give up." Pain says. "Give up on making me give up!" Naruto screams as he forms a Rasengan in his hand and runs towards the three. He got to them before they could react.
"Senpo: Rasengan..." Naruto says coldly and drives the dense chakra ball into the baldie. The crunching sound of metal crumbling spread through the battlefield. A shocked expression forms on the man's face before it goes limp. "See... All I'll have to do is this two more times," Naruto says with a stone cold expression. "I must admit... You are very fast. But you are not faster than me," Pain says as he appears behind Naruto and reaches his hand for Naruto's neck. Naruto weaves his head to the side. "You forget I can feel your chakra moving," Naruto says as he grabs onto the arm and throws the body over his shoulder and into the ground. "Impressive strength. But now I have full access to your body," The Pain says from underneath him. Pain moves the arm that Naruto wasn't holding onto and places it near Naruto's chest. "Shinra Tensei," He says, and the feeling of the world turning on Naruto is overwhelming. He gets flung away from the traped body he had under him. He lands on the ground. It would have hurt him if he wasn't in Sage Mode, but he stands up and dusts his shoulders off. "Your Jutsu is strong. But it isn't stronger than Nature itself," Naruto says as he locks onto the other body of Pain. Naruto runs over with as much speed as he can. He throws a punch. But the man dodges the punch without any difficulties. So the Pain he had thrown over his shoulder was up again. He was sure that throw was enough to break the man's back. And if not that, at least a leg or two. The Pain's must not feel any pain.
Naruto flashes away from the two. He reassesses the battlefield again. The Pains were standing back to back with the main Pain turned to the opposite side of Naruto. The other Pain was looking for Naruto. But it seemed like he hadn't found him yet. "Your share visual links. Let's do genjutsu then," Naruto says as he forms his hands into the tiger seal. He had read about this technique in the Senju library, but he had never had a reason to use it. "Kokuangyo no Jutsu!" Naruto says. The Pains find themself in infinite darkness. Naruto takes a deep breath. This jutsu sure takes a lot out of you. Naruto walks over to the two of them. He forms a Rasengan in his hand. "Only one left..." Naruto says as he drives the Rasengan into the long-haired man's stomach. It was quicker than either of them could react to the change in Naruto's chakra. The man flies and bonuses on the ground before he dies.
The main Pain perks up when he feels the influx of chakra from his second to last body going offline. But he still cannot see anything around him. Thanks to Naruto's genjutsu. Finally, Naruto walks over to the last body of Pain. He was looking around with his fists raised to be ready for anything Naruto would throw at him. Naruto reforms a new Rasengan. "It's over..." Naruto says as he smashes the Rasengan into the stomach of the last Pain. Inoichi and his team, consisting of a Hyuuga and Shikaku, jump down to meet Naruto in the centre of the massive crater that used to be the main square. Naruto was looking over the village, really taking in the destruction. A single tear rolls down his cheek. The black markings of Sage Mode began to fade away.
"I'm sorry I wasn't here to stop this," Naruto says to the men. "No one could have predicted that he would take the fight here, Naruto," Inoichi says as he places a hand on his shoulder. "Where is Ino, by the way?" He asks. "I left her a few clicks from the village in the heat of my pursuit. I didn't want her to see the state the village had been left in. I'll get her when this is all over," Naruto explains. A few seconds of silence lays down over the two men. "I have to finish this. The real battle has only just begun," Naruto says as he squats down and pulls out one of the black rods from the last Pain's body. He inspects it thoroughly. "Alright. Let's assemble a strike team to take him down once and for all," Shikaku says. "No... I have to do this alone. He said something that I need to investigate. Alone," Naruto says with finality. "Don't be stupid, Naruto! You have already done more than anyone can ask for. Now rely on the village that remains and let us help you," Inoichi tries to counter.
"I already told you. I'm going alone," Naruto says seriously. He showed some real steel, but the underlying threat that he would stop them if need be was thick. He didn't want to threaten anyone from Konoha, but if it was the only way for him to get a chance to settle this alone, then he would do it. "Inoichi. Let Naruto handle this alone. He has earned the right to talk with the man who killed his master," Shikaku says as he places a hand on the older blonde man's shoulder. "Fine! But call for us using Katsuyu if you need any help," Inoichi finally acquiesced. "Of course," Naruto says as he closes his eyes and the black markings of Sage Mode reappear. He takes a deep breath and stabs his hand with the rod. He cringes slightly at the pain, which was odd to feel in Sage Mode. He pinpoints the location in a few seconds. "I'll be leaving now. If I am successful, we will no longer need to threat over the Akatsuki. If I am not... then I do not know what will happen..." Naruto says before taking off.
Naruto was going through the forest while absorbing more nature chakra. Just in case he needed to fight again... He didn't know what he would say to the man who destroyed his village. He wasn't even sure if he would be able to let the man talk at all. Naruto lands near a fake tree. He takes a deep breath and enters the belly of the beast.
"I see you have come, Kyuubi. I felt you tracking my position through the rods," A man's voice says as soon as Naruto steps into the tree. Naruto takes his position in front of the two Akatsuki members in the tree. Pain's real body was so malnourished that Naruto could see his ribs, collarbone, and clear lines around the shoulder. Naruto's mind raced with diagnoses for what could have caused him to look like this. He looks them over. The coldness in his eyes was enough for Konan to feel chills down her back. His chakra was overwhelming. "You said you were working for peace... Why would you destroy the leaf if that is your goal?" Naruto asks sternly.
Pain took half a second to recompose himself after feeling the chakra vibrations in his voice. "Well..." Naruto says sternly. "Jiraiya-sensei always preached that war would stop when people put aside their hate and empithiesied with eachothers pain. That is why those who have felt pain, real, true, suffocating pain should be the ones leading the move for peace," Pain starts. "That is what Jiraiya-sensei thought. But that way of thinking is flawed and would never work in the real world. People aren't that understanding. They refuse to empithise with even their own people. They send their own people to die in wars that would just benefit their own countries perpatuating the circle of hatred," He continues. "Even what you are doing now is just pushing your hatred onto me. You are looking for someone, anyone to take the blame off attacking your village and killing all those people. You forget that the leaf was the ones that fought devastating wars in the Amegakure. Even if our village wanted to stay neutral you bigger villages couldn't let your own precious countries bear the burden of war so you used the smaller nations to bear that burden. You Konoha dogs killed my mother and father. We weren't even Shinobi!" He screams. "I see... I am sorry your family got caught up in the war..." Naruto says. "Well! What good does your sorry get me! All I have is pain!" Pain says.
"You say peace is impossible, and yet you do this to make peace! You can't say one thing and do another!" Naruto counters. "We have the same goal... We had the same teacher... I am sorry you warped Jiraiya-sensei's teachings cause now I need to stop you with all my might! I will find a way to make a lasting peace!" Naruto says with just as much conviction as Pain used in his own speech. "How can I trust you!? How can I trust that you will not chance!?" Pain screams out. "I have a name. A presious heirloom passed to me by my teacher. And with that heirloom I inheritet a dream, a responsiblity to try with all my might to find a way to live in peace," Naruto says. He reaches into his pouch and pulls out a sealing scroll. A book pops out with a puff of smoke. "Jiraiya-sensei wrote this book with a student in mind. From what I have heard I am guessing you were that insparation. The name of the charachter in this story is named Naruto. That is where my parents got their insparation to name me," Naruto says. "I see..." Pain says. "If I strife from this path... then this isn't the life of Senju Naruto anymore. Than it becomes something else, I will swear to you that I will do everything in my power to make a lasting peace and I won't stop until I have some sort of answer to help the world into a path of peace," Naruto swears. "And I never go back on my word, that is my Nindo!" Naruto says. Pain was taken aback by Naruto's lecture. "Nagato... My name is Nagato... I want you to remember it as I fix the wrongs I have done to Konoha," Nagato says as he begins to go through the hand seals of a Jutsu. "No! Nagato! You cannot do this! Your chakra is too low!" Konan says as she tries to reach out to stop her leader. "Stop it, Konan. I have to right the wrongs I have done to this village. I chose to lay my trust in this boy. I have lost my path. But that does not mean I have to stay on the wrong path for the end my life on it," Nagato says as he finishes his sequence of hand seals. "Gedō — Rinne Tensei no Jutsu..." he says. Nothing happens in the tree. Then suddenly, Nagato begins to age. "What did you do?" Naruto asks. Katsuyu pops up from Naruto's collar. "The villagers are coming back to life! I have never seen anything like it!" She says. "Nagato's dojutsu is the gate between life and death. He used a jutsu that can bring the dead back life," Konan explains. Naruto falls to his bottom in shock. "Thank you for giving my faith back, Senju Naruto. I will look over your progress from the next life. And pray that you find a way," Nagato says before he closes his eyes for the last time.