Summary: Time was a funny thing. Its ever-spinning wheels never stop, and are only disrupted when a foolish mortal time-traveler dares to pluck at the timeline's strings. They are dealt with anyways, and the 'glitch' is fixed, because some things were just meant to be. But there can be exceptions, Young Nagato Uzumaki learns of this and his role in time when he meets young Naruto and Sasuke back when they were genins.

Chapter 1

Naruto's Story

Nagato Uzumaki had always been fascinated by his mother's life story. It was like she came out of an anime. In contrast to the darkness of the ninja world now, the world in Naruto's time had been much, much brighter. A world where all the ninja villages ever worried about were just missing ninjas and that they were lucky enough if they managed to retire from ninja duty alive. These days, everyone lived in constant fear of the poorly sealed Jubi, and they were only lucky enough to even be born. Food and life itself became rare after the Fourth Great Ninja War. The best chance of survival was to settle in large groups, or in the Hidden Villages. The Hidden Village with the largest population was Konoha, and even that was a little under five-hundred people. Nagato had never seen more than this number of people in one place.

The little raven-haired boy would always make his way to the Hokage Tower, where his mother always whittled her deteriorating life at doing paperwork and trying to keep the village more or less alive. Then he'd sit on the old lady's lap and ask her to tell her story…again. Naruto would chuckle and take a break from Hokage duty to tell Nagato of the days when her teammates were still alive and young. Nagato would hang onto every word, clapping at every achievement and crying at every injury or death. He loved hearing about his mother's best friend, Sasuke Uchiha, and wished he was still alive so he could meet him. Then he popped the question almost every parent dreaded answering.

"Kaa-chan, where did I come from?" Nagato asked innocently.

Deciding the ten-year-old was old enough to understand, Naruto started to explain to Nagato just how he came to exist in this war-torn and depressed world.

Flashback…

"Orochimaru…" Naruto's raspy and abnormally aged voice was heard behind the Snake Sannin. Orochimaru turned his head a full one-eighty degrees to face the Sixth Hokage, which made the blonde uncomfortable.

"Oh Hokage-sama, what a pleasure it is to see you so soon after your…request." The snake-eyed man greeted. "And the Jubi seems to have aged you quite well." Orochimaru nodded at the jinchuuriki's aged face. Naruto looked over eighty years old when she was actually thirty-two.

"Is it ready?" Naruto asked, getting straight to the point.

"Ah yes, the replacement for the Jubi's container." Orochimaru snaked (no pun intended) his way to a crib in the corner and lifted out a small bundled child with a tuft of black hair on his small tan head.

Naruto couldn't hold the Jubi inside her forever, just like how Sasuke died barely a year after being implanted with Obito's and Madara's Rinnegan to keep safe. Of course, she had to bury the most powerful eyes along with her best friend. Having Uzumaki blood, Naruto was more resilient in holding the Ten Tail's chakra and even that was taking its toll on her. Neither she nor Sasuke were Rikudo Sennins, they would never be able to hold the power he held for very long, as was seen when two certain Uchihas were defeated by their own power at the end of the Fourth Great Ninja War. Thus, she had to turn to Orochimaru for a vessel more volatile than her.

Naruto smiled as the infant was presented to her. He had tan skin and whisker-like birthmarks just like her own, as expected of a clone made from Naruto's DNA and not a Shadow one at that. His eyes were closed in sleep so Naruto couldn't tell whose eyes he had. But Naruto just had to wonder, just where did the dark raven hair color come from?

"Did you use anyone else's blood?" the Sixth Hokage asked the Sannin in suspicion. Orochimaru chuckled in embarrassment.

"Ah so you found out. I couldn't make a complete clone based off your DNA alone. I had to use someone else's as well."

"Whose?"

"Sasuke Uchiha's"

Naruto's eyes widened. She couldn't believe Orochimaru still had a DNA sample of that dead bastard even after all these years. Then again, this was Orochimaru here.

"Does that mean he has the…?" Naruto asked, hoping against hope that the new Jubi jinchuuriki did not have the Sharingan. Too much hatred erupted from those cursed eyes. Sasuke would probably be furious if he knew he had an offspring to carry on the Uchiha curse.

"No, not quite." Orochimaru reassured. "Although…Let me tell you a story. The Rikudo Sennin had two sons. One inherited his 'eyes' while the other inherited his 'body'. The son who inherited the Rikudo's 'eyes' came to be known as the Uchiha Clan ancestor, and the son who inherited his 'body' came to be known as the Senju Clan ancestor. Throughout the years, a part of the Senju clan broke off into a separate clan called the Uzumaki. The reason why Sasuke-kun died of the Rinnegan was because, while he met the 'eye' requirements, he didn't have the 'body'."

"What does it have to do with this?" Naruto indicated to the baby snoozing in her arms.

"Think about it, Hokage-sama. If the descendants of these two clans were to procreate or, in this case, if they created a human being with their mixed blood then the offspring will have both the 'eyes' and the 'body' of the Rikudo Sennin."

"So he has the-" at that moment the infant woke up, eyelids flashing open as they revealed a ripple-like pattern which spreads over his eyeballs, with light purple irises and sclera.

"Rinnegan." Orochimaru finished. Naruto fell silent, staring at the godly eyes set in the face of this frail and innocent baby.

"Hokage-sama, I believe it's time for the sealing." The Snake Sannin broke the silence. Naruto frowned, realizing what she was about to do to the little boy in her arms. But just like her father had faith in her, she would put her faith in her son.

Flashback End…

"Kaa-chan, are my eyes bad?" Nagato asked sadly as said eyes bore into his mother's own, almost like they were peering into her soul. Naruto smiled at him reassuringly.

"Of course not Nagato-chan, they're just very special."

"But, the other kids, they always call me names like 'freak' or 'demon'." Naruto scowled at that.

Nagato had little to no friends, partly because he preferred to stay away from large groups and talking only when he had to. 'Just like a certain anti-social bastard.' Naruto thought bitterly. But the biggest reason for not having any friends was because of his eyes, which were abnormal and dangerous as everyone believed, and the fact that the Ten Tailed beast resided inside his gut. Naruto couldn't do anything about the villager's hostility towards him; being the Hokage, she had little freedom. At this point in time, Naruto knew how the Third Hokage felt back when she was Nagato's age.

"Nagato," Naruto addressed. The boy with shoulder-length black hair looked up into Naruto's azure-blue eyes. "You're not a freak, nor are you a demon. Don't listen to anyone who tells you otherwise. Just remember, that I'll always love you."

And Nagato believed her. With watery eyes Nagato hugged his mother, still sitting on her lap. Naruto ruffled the raven's hair. He looked so much like Nagato with the shoulder length hair and the eyes, but with tan skin, whisker marks on his cheeks and black hair. Because of their similarities, Naruto had named her son after her sibling disciple.

When Nagato calmed down enough, Naruto told him about the Jubi, how it was sealed into him because no one else could hold it. It wasn't the best seal because Orochimaru was the only seal master for miles around. If it were Minato or Jiraiya, people would've slept better knowing the Ten Tails still existed. Not to say Orochimaru was bad at sealing, just that he wasn't quite as good as the former two. Nagato took the news surprisingly well, as if he suspected it. Then Naruto went back to recounting the tales of her life. She repeated it so many times Nagato knew it by heart, but it didn't stop him from wanting to listen to Naruto's story over and over again. Whenever Naruto spoke highly of someone, Nagato would believe them to be a god. Such people were those who Naruto had respected and adored during her lifetime; like Kakashi, Jiraiya, her father Minato, Killer Bee, Iruka, Itachi, the entire Konoha Eleven (most of whom were now dead), and even Sasuke.

When Naruto decided enough story-telling was enough, she set down the raven and Nagato ran off for another ninja lesson with his private teacher, Konohamaru Sarutobi. Naruto leaned back into her seat and sighed before going back to doing paperwork. Even with the Jubi gone from her gut she knew she didn't have much longer to live before she died. When she did, Konohamaru would have to be ready to take up the title of Kage.

Naruto had just one regret in life. She never got to tell Sasuke how she really felt about him. Instead, she got a mini-mix of herself and the bastard she called her best friend. Technically, Nagato was Naruto and Sasuke's child, which was…weird, but felt right at the same time. Naruto was sure Orochimaru did this on purpose, just to freak the blonde out. But if Nagato was happy, then Naruto could die happy. He was her son after all.

Naruto hoped Nagato would turn out the way she did, respectful of peace and upholder of justice. Who knows? One day he might even become Hokage and rid the fear and poverty the people of today lived in.

Two Years Later…

Naruto lay on her death-bed in the Konoha hospital, her life and soul seemingly drained off her. Twelve-year-old Nagato sat next to her in a chair, tears threatening to fall and praying to whatever god out there that Naruto would not die. It was inevitable; of course that Naruto would die. During the time the Jubi was sealed in her, Naruto aged twice as fast as everyone else. The Bijuu ate away at her life, never caring if she died or not, it cared for only its freedom. As Naruto neared her time, she turned to Nagato.

"Nagato, even though our ninja world seems to be at peace, evil will always be reborn and spring right back up with some sort of evil plan in mind. So, when they do, promise me you'll fight them. Fight evil for the sake of peace and justice. If there is such a thing as peace, find it and grab hold of it." The blonde rasped out as Nagato fought back his tears.

"And, I know you might not have many friends now," she continued "but, one day, you'll find precious people who will worm their way into your heart. Remember, and this is a quote from one of my late senseis, those who break the rules are scum but those who abandon their friends are worse than scum."

Nagato's tears were freely falling now. "Nagato, keep on living." And with that, the Sixth Hokage of Konohagakure, the former jinchuuriki of both the Kyuubi and the Jubi, the daughter of the Fourth Hokage (AKA the Yellow Flash) and the Red Hot Habanero and the mother of Nagato Uzumaki took her last breath in the hospital bed with her biogenetically engineered son by her side.

Nagato broke down into sobs as the nurses and doctors came to take her out.

"Kaa-chan..." he whispered.

…

The young Uzumaki stared at the Hokage Monument, at all the Hokages that that had ruled over and kept the Village Hidden in the Leaf safe. The raven learned all their names; the First being Hashirama Senju, the Second Tobirama Senju, the Third Hiruzen Sarutobi, the Fourth, and his grandfather, Minato Namikaze, the Fifth Tsunade Senju, the Sixth, his mother, Naruto Uzumaki, and the Seventh whose face was currently being added was Konohamaru Sarutobi.

Sitting on a pole (coincidently, the one Naruto stood on when she first came back from her training trip with Jiraiya), Nagato reminisced all that Naruto had ever told her. The young Rinnegan bearer thought about her last words. The ninja world right now wasn't really at war, but it wasn't necessarily at peace either. People were still dying, either died of starvation or killed for one reason or other. He remembered his blonde mother saying that hatred bred wars and as long as a ninja system existed, hate existed. Thinking of ninja systems, Nagato's thoughts drew to the mysterious Rikudo Sennin who had been the first ever shinobi and created the ninja system in the first place.

Sighing and closing his eyes, the raven dove deep into his mindscape the way Naruto had done when she had the Kyuubi. He had never done this before, as his mother always told him not to, but it was about time he met his prisoner who he didn't realize he held captive until Naruto told him about the war and the Jubi.

When Nagato opened his eyes, he was met with a dark room similar to his own in the apartment he shared with his Kaa-chan. However, it wasn't the same. The layout was different, and there was a big sliding glass door positioned in one wall, which seemed to lead to a balcony. Nagato slid the door open and stepped in, or out depending on where he was. Squinting in the dark, the raven made out that the balcony-like platform was far larger than he expected, he couldn't even see the edge. The sky was black, no stars and no moon, just plain black. And there, smack in the middle, was the largest cage Nagato had ever seen in his entire life. Even the Hokage Monument looked smaller than an ant compared to the sheer size of this steel prison! The inside was dark and almost imperceptible. The only thing the boy could see was a giant pole that pierced the center of the cage and that…something was tied to it with chains and pierced into it with giant spikes connected to the chains. That something was grunting and shifting around from its uncomfortable position against the pole.

Nagato warily stepped closer to the cage against his better judgment. The thing inside stopped moving and Nagato's breath hitched. It opened its one eye, which took up most of its head. That unique glowing red eye had four concentric circles with nine tomoe in the three circles closest to the pupil. It was like a mix between the Sharingan and the Rinnegan. Nagato silently cowered in fear at the sight of the monster before him.

"I knew you would come." its voice was deep and resounded throughout the mindscape, echoing off the walls. "It took you long enough to come here though."

"A-A-Are you the J-Jubi?" Nagato managed to stammer out. The Jubi's glowing eye stared into his own, piercing into him and analyzing his worth.

"No, I'm a cute little puppy wagging its tail and waiting to be fed." It snorted. Nagato scowled. He didn't remember Naruto saying that the Ten Tails was sarcastic, of all things. "Child, are you ready?"

"What?" Nagato glared at the beast, now with less fear. "I'll have you know I didn't come here to set you free. I just came to see what you look like!" he pointed defiantly at the caged beast. However his confidence was shot down when the Jubi glared at him.

"Of course, you come here with the intention of 'visiting', only to find yourself in another situation. It happens again and again and again." The Jubi sighed. Moving and shifting its body around more, Nagato froze with terror and mortification as he helplessly watched the spikes holding the beast fall out from its flesh and the chains around it loosening. Reaching out to the cage bars, the Jubi pulled at them, denting them so that it had an opening. And it did all this so easily.

"Your so-called 'seal master' is not worth shit. No seal made by someone other than the Rikudo Sennin could hold me. I only waited out this long until the time when you first come to 'see' me. I'm tired from this circle of time crap, someone needs to break it." A smaller clawed hand emerged from one of the Jubi's fingers. It wrapped around Nagato's small frame and hoisted him up. Nagato was still petrified but managed the willpower to speak out.

"What are you doing? Where are we going?" he called out, panic evident in his tone. The Jubi brought the boy up so he was faced with its eye.

"Nagato Uzumaki," Nagato flinched, he'd never classified the Jubi as one to call humans by their name. "I am going to make history, while you are going to break it." A distortion in Nagato's vision led him to believe that the Jubi must be using some sort of space-time jutsu on him. "Say hello to little Naruto for me." Were the last words Nagato heard before he blacked out.

As the great beast blasted Nagato to the past, it sent itself much further back. As its feet collided with the ground, it looked below itself. It found a man with a small goatee and short light-colored hair that spiked up in the front with two distinctive pieces of hair resembling horns. He wore a white haori with a high collar, revealing his necklace with six red magatama. He held a khakkhara, his ringed staff, and he lifted it in defiance against the Jubi. The Ten Tails smirked inwardly, knowing he would lose to this man; he'd done so countless of times.

'Good to see you again, old friend.' The Jubi thought before engaging in with the Rikudo Sennin a battle that would shake the earth and crack the mountains, the battle that started the history of shinobi.

…

When the distortion cleared, Nagato found himself facing a grassy floor several meters from her face. Eating dirt as he landed, he heard footsteps and human voices.

"Did you see that? He just fell out of thin air!" a very familiar female voice exclaimed.

"Dobe, people don't just fall out of the sky. There must be a logical explanation for this." A male voice was heard; it was mostly emotionless but held a hint of irritation.

"Is he alright?" another girl asked in concern, yet held an itty bit of suspicion.

"Hey, you, are you okay?" an older male voice asked Nagato as he pushed himself up on his knees, subconsciously raking his fingers down his fringe so that it covered his eyes. He always did that when in the presence of someone who wasn't Saru-sensei or his Kaa-chan. That way he would see them but they couldn't see his eyes. He stood up slowly.

Turning around to face the other presences he saw an older masked man with gravity-defying silver hair. He wore the standard jounin attire and Konoha headband across his forehead and left eye.

"I'm okay." He assured. The man smiled, or he looked like he smiled, Nagato couldn't tell with that mask on.

Looking behind him he saw three other kids who were around his age. One had bright pink hair, large green eyes, and fair skin. She wore a red qipao dress with white circular designs, with short sleeves, a zipper, tight dark green shorts, and a forehead protector positioned on top of her head which accentuated her face. The next person he saw was a fair-skinned boy who had onyx eyes and black chin-length hair. His hair was spiky in the back with bangs hanging on both sides of his face to roughly frame his cheeks. He wore a navy blue, short-sleeved shirt with a high collar and white arm warmers along with white shorts. His short blue forehead protector was tied around his forehead. The boy looked strangely familiar. The last person made Nagato's hidden eyes widen at the sight of her.

A blonde, long haired girl with blue eyes and whiskered cheeks stared at him. Her outfit consisted of an orange tracksuit with blue on the upper shoulders area as well as around the waist, a white swirl with a tassel on the left side, a large white collar, orange pants, blue sandals, and a blue forehead protector tied around her head proudly showing off her allegiance with the Leaf. She was like the younger version of Nagato's Kaa-chan.

"Hello~" the masked jounin waved in her face, snapping Nagato out of her shock. "Anyone in there?"

"I'm sorry, I was just…thinking." Nagato apologized.

"Is that so?" the man mused, uninterested. "But I was asking you who are you? And do you mind explaining to us how you fell out from the sky?"

"Um…My name's Nagato." The jounin nodded, not pressing him for his surname. "As for what happened…I'm not sure I understand myself."

"Who's your sensei?"

"I don't…know."

"Are you even from Konoha?"

"I…can't remember." Nagato figured that if he led them to believe he had a memory problem, they might let him off and stop asking questions.

"Oi, oi, oi, what do you mean you can't remember?" the mini-Naruto asked.

"Baka Naruto, it's obvious he has some sort of amnesia!" the pink-haired girl screeched. Now Nagato knew the blonde was Naruto. How she became younger and how she didn't recognize him, he didn't know. The biggest question was how she was still alive.

"Aww, but Sakura-chan…What's amnesia?"

"Dobe, amnesia is a deficit in memory caused by brain damage, disease, or psychological trauma. Since he fell on his head, it's quite clear his amnesia came from brain damage." The boy dressed in blue and white said.

"That's right Sasuke-kun. You're so smart!" Sakura fawned. Nagato froze. Sasuke was his other parent, but he was supposed to be dead, right? What's going on?

"If that's the case then we'll have to get him to the hospital." The silver-haired man swooped Nagato up, carrying him bridal-style. Nagato struggled a little against his hold in embarrassment but the man only tightened it. "While I carry him there, you guys continue your spar." And with that, their sensei body flickered from the scene.

"Huh, it's not everyday people fall out from the sky." Naruto broke the silence.

"Of course not, you baka!" Sakura scolded.

"Hn, whatever, let's continue where we left off, Dobe." Sasuke directed at Naruto, taking a taijutsu stance.

"Yeah let's continue my kicking your ass!"

"That's not what was happening ten minutes ago."

"Teme!"

…

Nagato opened his eyes. When had he fallen asleep? Sitting up on the hospital bed, he noticed the paper-like feel of the hospital gown on his form and bandages around his head. Why was he in the hospital? Memories of what happened before he blacked out came flowing back to him. Alone in a hospital room gave Nagato the time and sanity to think this over. Naruto was alive and apparently younger, Sasuke was alive and around the same age, they seemed to be genins still. What was going on?

Looking at the window, Nagato's eyes widened at what he saw, or more like, at what he didn't see. The hospital window gave a clear view of the Hokage Monument, where the construction of the Seventh's head was supposed to be undergoing. However, absolutely no construction of any kind whatsoever was going on and the monument was missing two heads, the Fifth's and the Sixth's.

This gave Nagato more clues of what to think. His parents were alive, not to mention kids, and the ruling Hokages went up to the Fourth. If Naruto was born, then that meant the Yondaime was dead. In short, the Jubi sent Nagato back through time. Nagato grew uncomfortable. He was aware of paradoxes, and he felt that for every moment he spent here in the past, the present was changing bit by bit. For better or worse he would never know. It would be hard not to change anything as he didn't know how to get back to the present, not to mention that the Hokage would probably want to see him, which led back him back to the present reality at hand. A knock was heard from his hospital room door.

The door was opened by a light-skin old man of below-average stature with short spiked grey hair. He sported a goatee, a prominent crease across his forehead, a few wrinkles, a wart near his left nostril, and a few liver-spots. He wore the official Hokage uniform — consisting of the customary hat and haori, along with a red, full-length kimono that was tied using a white sash. This man, Nagato recognized, was Hiruzen Sarutobi, Third Hokage of Konohagakure. Seeing the boy awake, Hiruzen advanced towards him.

As the Sandaime approached the raven, Nagato groaned mentally when he realized that the old man would probably ask questions. Then he remembered he was supposed to have amnesia. 'Just feign memory loss.' He told himself. Then it hit him, why was the Hokage of all people here?

"Hello, young man." The Third greeted as he sat down on a nearby chair. "I trust that you feel better now." Nagato nodded slowly. "Ah, then allow me to ask you a few questions." Nagato was prepared for this. Hiruzen attacked him with the first question.

"What's your name?"

"Nagato, I think." Hiruzen nodded in understanding.

"Where do you live?"

"I…don't really know."

"Do you have any family?"

Nagato hesitated before answering, "I don't know, maybe I don't."

"Do you know who I am?"

"No, sir."

"I'm the Third Hokage of Konohagakure." Nagato's face struggled to remain indifferent, his eyes unreadable as they were still covered by his bangs.

"What all do you remember?" the Sandaime continued.

Nagato stayed silent, as if in thought. "Nothing else, just my name."

Hiruzen nodded in confirmation. "You hit your head pretty hard, even though the reasoning behind it is unknown, so I don't blame you for your memory loss. Rest here, tomorrow in the morning one of my men will search your mind to help you with your amnesia problem." And with that, the Third Hokage got up and left Nagato to his thoughts.

Nagato leaned back down on his bed, pondering over what he should do. He never thought he could be such a good liar, but lies only went so far. His game would be up when an interrogator searched his mind and found out the truth. The present would be completely changed if all the information he held spread amongst those in the past. The raven heard voices outside his door. Said door was opened with such force, it almost flew off its hinges.

Turning his attention to the trespasser, Nagato saw the young, orange-wearing blonde that was the younger self of his mother. Followed by her were her teammates, the pinkette and his father, and then their teacher, who Nagato just realized was the famous Kakashi Hatake.

"Hey, hey, you're awake, right? Did they check your head for anemia?" Naruto asked excitedly. Nagato wondered if she was always this hyper when she was young.

"It's amnesia, dobe." Sasuke corrected.

"Whatever, teme. So, umm, Najuke, was it?"

"Nagato actually." Nagato corrected.

"Oh, Nagato, so are we, like, relatives or something?" Nagato's eyes widened behind his bangs. How could she tell? "Ya know, 'coz we both have these whiskers and stuff." Naruto pointed to her whiskered cheeks and then to Nagato's whiskered cheeks. Nagato gingerly touched his cheeks.

"I still don't remember anything." He lied. Naruto looked defeated for a moment there; she really hoped she had at least a distant cousin or something out there. Any kind of family, in fact, to remind her she wasn't totally alone. Then she sprang right back up, the aura of happiness emanating off her. Naruto didn't like feeling sad or negative.

Nagato and the rest of her team watched her fluctuating emotions. Nagato remembered his mother's last words. 'If there is such a thing as peace, find it and grab hold of it.' Here was the only chance at peace Nagato would ever find. He'd change the future, little by little, and turn the odds in favor of the ninja world. He'd have to do it alone, and with no one else knowing. And this would require a great deal of careful thinking and precise moves, like a game of shogi.

Nagato nonchalantly ignored Naruto's bickering with her teammates in favor of planning out his next move, how to avoid the inevitable mind reading that was to happen the next morning.

…

AN

Whew! This took a while to write. Originally, Naruto was supposed to be male and Nagato female (with the name being Konan) but I figured I Ioved SasuFemNaru too much. For equality I changed the OC's gender too. The timeline, in which Nagato has fallen, takes place sometime after the Wave Mission. Just thought you should know. Constructive criticism and reviews are appreciated. :3

Dragonoiya