AN:This chapter is all about things that changed before Naruto's birth. You could almost call it the second part of the prologue.
2 years until Kyubi attack
Minato sat on him and Kushina's bed channeling chakra into her seal in order to repair the damage done to it during the day. This had become a nightly routine ever since Kushina had seen Nagato's Rinnegan. The beast within the seal went ballistic shouting about how impossible for anyone to have those eyes, and was fighting to escape with more vigor than ever. He demanded blood, it effected Kushina's abilities in the field drastically. It was already hard enough to contain the strongest Biju in the midst of battle, but now that it was more pissed off than usual it was damn near impossible. Along with the fact that Konoha is at war right now doesn't bode well for the kunoichi.
"Ne-chan, I think it's about time that the Kyubi and I bury the hatchet. I don't know what its problem is, but this is getting ridicules." Nagato said walking through the open door to the couple's room. He was now tall for a seventeen year old, while he was now in better physical condition he was still scrawny.
"No, you are not entering my mindscape and that's final." Kushina had heard this before, and every time she gave a similar response.
"Sorry Ne-chan, but this time you don't have much of a choice. The Kyubi is killing you, maybe not directly, but if you continue to fight with it going crazy like this you aren't going to make it to you and Minato's wedding. I'm sorry, but you have to understand that this is for your benefit." Nagato said before she felt a blow to the back of her neck, and passed out. "Minato-san, you know the drill, I just hope that she can forgive us for this." Nagato said activating the powers of the Human path to force his way into his sister's mind.
In Kushina's mindscape
"Alright Furball what's your problem with me and my eyes?" Nagato asked in a cocky tone as he put Kushina in a clear dome structure to prevent her from screaming, or trying to expel him from her head.
"You dare to speak to me, the Kyubi no Yoko, as if I'm some common house pet! I can't wait to pulverize you in between my fingertips!" The Kyubi started struggling more fiercely than before to break free.
"Answer my question before I rip your memories out and find out for myself! I don't know what your problem is, but it's putting my sister in danger. If she dies I'll track you down when you reform. I'll personally seal you onto a rock that's reinforced with more seals to prevent your escape, and that's where you will remain for all eternity. You think that this seal is uncomfortable, wait until it doesn't have senses for you to experience." Nagato was blaring killing intent on par with the Biju at this point.
"Shut up you mongrel! You may have his eyes, but you can't compare to my father who could actually follow through with the threat you just made!" The Kyubi managed to get a single tail free for a short period of time before it was staked back to the boulder he was strapped to.
"The Rikudo Sennin was your father!? Wait, You have a father?!" Nagato was surprised to say the least.
"Why do I even bother communicating with you Ningen?" The Kyubi seemed to calm down at Nagato's childish outburst.
"Seriously why do you want me dead so bad? I didn't do anything to you. I just want to protect my Ne-chan." Nagato was hoping that since the Kyubi had calmed down he could get an answer finally.
"Tell me Ningen, what's your goal in life?" Nagato wasn't expecting the Kyubi to ask him a question
"Why do you want to know?" Nagato asked in response.
"TELL ME! I refuse to speak further until you tell me Ningen." The Kyubi shouted.
"My goal is to end all wars, unite the five great nations, and create a world where Jinchuriki aren't needed. A world where people don't have to watch their family slaughtered for being mistaken for enemy soldiers, a world where fear won't lead to the eradication of a country simply because they don't choose a side in a war. I'll break the cycle of hatred that's taken hold of this world." Nagato said with conviction.
"You aren't lying, but how do you plan to bring this world without wars you speak of about? How do you plan to bring about the peace that you seek?" The Kyubi asked.
"Peace… I don't know how to get there… but… but someday I'll break the curse. If there's such a thing as peace, I will find it!" Nagato said the same thing that he'd told Jiraiya a few years ago when he asked a similar question. "These eyes of mine let me into the minds and hearts of people, so that's a start."
"Boy your eyes do more than that. The power you contain could bring this planet to its knees if used for that purpose. I wanted to kill you so that you didn't use my father's power for evil and taint his legacy. Tell me, which is more important in the quest for peace, love or power?" The Kyubi continued asking his questions.
"I don't know. Love is important, but you need power to protect the peace from those who would seek to destroy it. I guess that both are equally important." The Kyubi stopped struggling after hearing this.
"Boy you've just earned my approval, don't disappoint me. If you do then you and your entire race will regret it. Have a seat we have much to discuss about your eyes, and please call me Kurama." The Kyubi surprised Nagato and Kushina for the second time that day when he smiled and gave out his real name.
1 year until Kyubi attack
"Okay team Kakashi, your mission is to destroy the bridge our enemy needs for their supply lines. Expect minor resistance, most of their forces are on the front lines, but it would be foolish to leave a bridge that important undefended." Minato said pointing at a map indicating the position of their target.
"Hai sensei!" Kakashi, Obito, and Rin said in unison.
"After your target is destroyed retreat immediately, team Ame is on their way to assist you in your escape. I'll accompany you guys to the border, after that I have to go back to the frontlines. Kakashi is the leader of this operation."
Several hours later.
"They've got Rin, We've got to go after them!" Obito said after a short encounter with two enemy Jonin that beat him and Kakashi, and kidnapped Rin.
"No. We continue the mission. She's a medic nin so even as a prisoner she'll be treated well." Kakashi said emotionlessly.
"She's our teammate! And she's a female, they'll probably rape her endlessly despite the fact that she's a medic nin. I'm not going to let that happen!" Obito was angry to say the least.
"We have our orders. Shinobi who disobey orders are trash." Kakashi said sternly.
"Then I'll gladly become that kind of trash. I still to this day think that the White Fang is a hero. Those who disobey orders are trash, but those who abandon their comrades are worse than trash. I don't care if you're leader, I'm going to save the woman I love from a fate worse than death. If you want to join me then fine, if not then just go away!" Obito turned around and began to walk away. Kakashi was astonished that anybody thought of his father in a positive manner, and was beginning to question his beliefs in the rules.
"So Rin got captured?" A new voice said as three cloaked figures landed between the two arguing boys.
"Yeah, I'm going to go get her. You got a problem with that Sempai?" Obito said to the figure that asked.
"No, but I do have one question. What the hell are we waiting for? We've got a rescue to mount!" Nagato said removing his hood, as did the two with him revealing Yahiko, and Konan.
"Right Sempai they went this way." Obito and team Ame left to pursue the kidnappers, leaving Kakashi to ponder for a while before he too turned to follow them.
At the enemy base
Each of the four Konoha shinobi there to Rescue Rin were stationed in different positions around the Earth Dome that the Iwa nin were using as a base.
"Okay we can do this. I can do this. I going in." Obito said to motivate himself.
"Going into where exactly?" A voice asked behind him.
Obito turned around only to see nobody was there. That's when he felt something impact against his stomach knocking the wind out of him. The Iwa nin that snatched Rin earlier then appeared, he had been using a Genjutsu to become invisible.
'Shit! I'm going to die here, and I haven't even told Rin how I feel yet.' Obito was thinking this when Kakashi roundhouse kicked the Iwa nin into the trunk of the tree that they were standing on.
Kakashi then charged his Chidori and charged at the Iwa nin, he missed his mark grazing the enemy' side. He got his left eye slashed in the process. The Iwa nin turned invisible again cursing in pain.
"Kakashi! So you decided to join the fun after all?" Obito said sarcastically as Kakashi leaned on the tree and pulled out the medic kit that Rin gave him earlier to congratulate him on his Jonin promotion.
"Watch for the enemy damn it!" Kakashi yelled as he started to wrap his eye in bandages.
Obito turned around and planted a kunai in the heart of the enemy not realizing that his Sharingan had awakened.
"How? What's with your eyes? Bastard." These were the last words of the Iwa nin as he fell to the ground dead.
"We heard some commotion, are you two alright?" Nagato asked as team Ame landed on the tree branch with Kakashi and Obito.
"What took you so long?" Obito to asked angrily.
"We were searching for an entrance, and we found one." Nagato said pointing towards the rock dome.
"I think Konan should stay here with Kakashi and tends to his wound. While you Obito and I go to retrieve Rin." Yahiko said to Nagato.
"Yahiko is right. Kakashi isn't going to be much help with that bleeding wound, and Konan knows basic medic jutsu. Besides there's one of him and three of us, this should be pretty easy." Nagato said.
After a small debate the five shinobi came to decision. The decision being that that plan was the correct course of action. So Nagato, Yahiko, and Obito moved in to confront the enemy nin and rescue Rin.
The three entered the Rock dome and immediately saw Rin sitting tied up and staring off into space, no light in her eyes. "Kai!" Obito yelled as he put his hand on her shoulder, breaking the Genjutsu that she had been placed under.
"You shouldn't have come here." Rin said looking up at her saviors.
"We couldn't just leave you here at the mercy of the enemy Rin." Obito said lifting her up and cutting the ropes that bound her.
"Run idiots! It's a trap!" Rin yelled as the rock dome began to collapse on top of them.
"Shinra Tensei!" Nagato yelled out as the pieces of the rock dome flew outward into the forest.
"Damn it! I thought for sure that would kill those fuckers." The remaining Iwa nin said as he pulled out a ninjato and took up a defensive stance.
Within seconds Yahiko was upon him, his hands growing, and his shin turning grey. The Iwa nin tried to block a punch that was aimed towards his stomach with his blade. This resulted in his ninjato scattering and him flying into a nearby tree. He then looked up to see Nagato who had removed his cloak, and shirt yell. "Armor of the Asura Path!" Nagato then began to transform, several mechanical markings began to appear on his body, he grew four extra arms as well as two extra faces in the sides of his head, and a long serrated blade grew out of his back from right under his shoulder blades. Meanwhile Yahiko completed his transformation. Yahiko's hands were about four times their normal size and had sharp claws, all of his skin was a dark grey color, his eyes became black with yellow irises, three horn like protrusions grew from his forehead, he grew a tail, and his back grew long spikes along his spine all the way down his tail.
"MONSTERS! GET AWAY FROM ME!" The Iwa nin screamed in fear before he died via Nagato's blade tail piercing his head.
"We're not done yet, I sense about a hundred chakra signatures approaching and we aren't expecting backup. Hide kids this is going to get ugly." Yahiko said transforming his hands, first he grew several extra fingers from random areas of his hands, and then his fingers opened up into a hollow honeycomb pattern.
"So crowd control techniques then." Nagato said opening his arms up to reveal hundreds of tiny missiles.
Several Iwa shinobi charged out of the woods only for the last words they ever heard to be "Sōkai Enpō!" (Twin Mystic Flame Cannons). As Yahiko began pelting them with golden flames imbued with sage chakra. They died upon contact with the flames, as it burns their chakra system. More tried attacking from behind Yahiko only for Nagato to neutralize them by firing several missiles at them. The rest of the battle was short since most of the remaining enemies retreated due to the sheer amount of destruction that the two in front of them are capable of.
Meanwhile Konan hid herself and Kakashi by blending in with the tree using paper. She had heard the enemies close in and decided to set a trap for the ones that retreated. She made several paper clones that littered the area with motion sensing paper bombs that were almost impossible to see. About sixty percent of the retreating enemies fell into this trap, leaving less than ten enemies to escape. The Konoha shinobi then completed their objective without any more enemy resistane.
3 month until the Kyubi attack.
The Third Shinobi World War was dying down, but that's the most dangerous time in a war between ninjas. Last resort methods start being used, methods that could lead to the destruction of entire nations.
"I'm telling you two you have to kill me." Rin said to her teammates.
"No Rin I can't do it." Obito said looking her in the eyes.
"I agree, Tell us what's wrong. What did they do to you?" Kakashi known on the battlefield as 'the One Eyed Fang' was worried.
"I can't, I mean I literally can't tell you. Part of it makes me unable to tell you. Just know if I go back to Konoha then it's all over. If you hadn't stopped them when you did I wouldn't even know what they did." Rin said trying to get her teammates to understand her predicament.
"Obito, I think that it's either a Genjutsu placed on her, or hypnotic suggestion. Your Sharingan should be able to break either." Kakashi said looking at his best friend.
"Why didn't I think of that?" Obito asked face-palming.
"Because you're an idiot." Kakashi said smiling under his mask.
"Hey!" Obito yelled causing Rin to giggle at her team's antics. "Okay Rin, I just need to say this just in case this doesn't go as planned. I love you, I always have, you don't have to say anything yet, I know you have feelings for Kakashi. I just wanted you to know." Obito said before activating his Sharingan while looking her in the eyes, causing her to freeze in place.
"Well?" Kakashi asked
"It's hypnosis. Not just on her either." Obito said not breaking eye contact.
"What do you mean?" Kakashi was confused.
"It looks like they made her a Jinchuriki for the Sanbi." Obito kept at it. "This is going to take a while, keep us safe Kakashi." Obito said before freezing like Rin.
"Well, looks like the fake pursuers are here." Kakashi said pulling out his tanto.
Two Hours Later
Rin gasped for air as Obito passed out from Chakra exhaustion. It took everything in him to undo the hypnosis on Rin and the Biju within her.
"Great, now we have to carry this idiot back to the village." Kakashi said sitting atop a rock with a pile of corpses next to it.
"No, I'll carry him. It's the least I can do." Rin said with a soft smile.
"Does this mean that you." Kakashi was cut off.
"Yes Kakashi. I was a fool not to realize how he felt, and an even bigger fool not to feel the same." Rin said leaning Obito on her shoulder. She struggled to move, so Kakashi helped support Obito as they made their way home.
Back at Konoha in the Hokage's Office
"So Kiri shinobi kidnapped Rin, sealed the Sanbi in her, and hypnotized both her and the Sanbi to destroy the village when she entered it. You two stopped it before the hypnosis on her was finished, and Obito undid all of it with his Sharingan." Minato the newly appointed Yondaime Hokage said not the least bit surprised that they would resort to this type of attack. He was surprised however that his student was able to reverse the hypnotism.
"Yes sensei. That is exactly what happened." Kakashi said.
"Rin let me take a look at your seal. It might not be stable just in case something like this happened." Minato said concerned for his student's welfare, as well as the welfare of the village.
"That won't be necessary, Isobu, the Sanbi, isn't going to be a problem as long as I take plenty of naps. He's actually a lot like a Nara, it's easier for him to not try to break out of the seal than it is for him to be hunted down and resealed." Rin said smiling.
"Still I want to make sure that it isn't going to just disappear on you." Minato said.
After taking a look at her seal, he applied some reinforcements to make sure that it didn't just break for no reason.
AN: For anyone wondering yes Kurama and Isobu are both going to be at least cooperative, if not friendly latter on. Also Yes Obito and Rin both survived, no Kakashi isn't getting a Sharingan his thing now is more or less surpassing his father while carrying on the legacy of the fang of Konoha, and now Konoha has two Jinchuriki. Next chapter will be hard to write so it might take a while.