Rinnegan: Tool of God.

A/N: Hey what's up guys, this is my Naruto story, it's my first Fanfiction but it's something I've been wanting to write for a while now, in this story. Naruto does have the Kyuubi sealed within him, but his whiskers only ever appear when he utilizes the Kyuubi's chakra, which won't be much at all during this story, since he'll have a godlike chakra pool thanks to his Rinnegan. Naruto is also aware of the Kyuubi inside but it's chakra doesn't leak into his.

Itachi will be a gray character, neither good nor bad, he'll take Sasuke of the coup on the night of the massacre, he also invites Sasuke to leave Konoha and join Akatsuki when he's ready.

Yes, he'll have Rinnegan; he'll be like Nagato would be if he hadn't used Kuchiyose: Gedō Mazō. So yes, he may seem obscene at points, but his normal enemies will be stronger as well; he'll make full use of his Rinnegan abilities as well as all 6 of the chakra elements, he won't use the Yin and Yang element much since I'll have to do some extensive research into what it actually is, Nagato will also train Naruto in the main Rinnegan abilities, like the gravity manipulation, the ninjutsu absorption and summoning that King of Hell, or whatever it is, that'll be used for interrogation. The basic summary of the story is:

Naruto's been abused by the villagers for the majority of his life, Itachi does the Uchiha massacre and sees Naruto getting a beating from the villagers while he's escaping, he watches as Naruto activates his Rinnegan and kills all of the villagers with ease. He decides to take Naruto with him. The story changes dramatically here, as I'm going to have Sakura go with them, since she's Naruto's only friend, yes, I know she's OOC so she'll be like the Part 2 version of Sakura, minus that ridiculous charade of lying to Naruto. It won't be a dark Naruto fanfiction; he'll be ruthless and cold at points, but also fun and cheerful. Kind of like Madara/Tobi. They go on to join Akatsuki, since no-one there can sense the Kyuubi chakra in Naruto, he has full control of it, since the powers of Naruto's unconscious Rinnegan have kept it at bay until then, so he uses it to do the same thing, basically the Rinnegan will suppress the Kyuubi and its chakra, Sakura and Naruto will be replaced by Karin and Sai on Team 7, Sasuke will leave for Orochimaru, he'll also take Karin with him and she'll be trained by Kabuto, training there in the medicinal arts. Oh yes, the Chuunin exams will be taken 3 years later than the one in the manga, so everyone will be at least 15, if not 16 years old. As you have to be 10 to be allowed into the academy in my story, so the Uchiha massacre will also take place 2 years later, when Sasuke is 9. I think he's older than Naruto, if he isn't, he is slightly in this story. Itachi will also be older, he'll be 15 when Naruto is 9, so he's 6 years older, just think about his normal ninja position before he left, and revolve them around the age difference, and you'll see what I mean.

Hiruzen is also ridiculously OOC in this chapter, but in my story Naruto is abused daily, so he has reason to be aggressive towards a selective group of villagers.

One more thing, sorry :D, but Naruto will have his bijuu removed at the start of the second chapter. Since the Rinnegan has kept the Kyuubi suppressed, Naruto's chakra pathways are the same as any normal person, therefore he can live without the Kyuubi as his body has not adapted to it. I know it sounds silly but I wanted to get it out of the way ASAP.

Disclaimer: I don't own Naruto.

Chapter 1:

Streets of Konoha:

"There he is! Get him!" One of the mob shouted.

Naruto, who was sprinting down the street, had looked back only for a second to discover he'd been spotted, his eyes widened as he noticed them sprinting towards him, several ninja gaining on him. He stumbled and cried out in pain as a shuriken struck his calf.

"Wait! Please don't!" Naruto cried out.

The mob merely smirked before descending on the small boy.

Elsewhere in Konoha:

"Hmm, it's Naruto's 9th birthday tomorrow, I wonder if anyone's going to celebrate that, and not the sealing of the Kyuubi, idiot villagers." Sakura, who was sitting on her windowsill, pouted as she thought about what might happen tomorrow. "I guess it'll just be me and him like last year then." She thought with a grim expression on her face.

Flashback

Naruto was strolling down one the main streets of Konoha, oblivious to all the glares he was receiving, ignoring all the shouts of "Demon!" and "You're not welcome here!", he already knew about the Kyuubi, since one of his attackers had already revealed it to him, much to the Hokage's chagrin. The offender in question had been silenced. Permanently.

He didn't know why but for some reason, today just felt like it was going to be good day even though tomorrow was his birthday, terrible things usually happen, so he decided to stop by at Ichiraku Ramen and ask Old Man Teuchi if anything interesting was going on that would provoke such a feeling.

On the way to the Ramen stand, Naruto's eyes glanced upwards towards the Hokage monument,

'One day I'll surpass you 4 and show the world that I'm not just a container for the Kyuubi but a strong ninja as well, then they'll regret all the horrible things they've said!'. Naruto thought to himself, his eyes still transfixed on the Hokage monument, he didn't a notice small pink haired girl step out from around the corner and walked straight into her, knocking them both over.

Sakura was shocked, one moment she was thinking about what Ino had told her about ignoring the bullies and showing off her forehead, telling her it was something that she should be proud of, the next moment she's on the floor with a strange blonde haired boy lying next to her, she was surprised when he stood up so suddenly and stood back, his arms raised above his face in a protective manner.

"I'm sorry, please don't hit me!" He shouted. Sakura slowly stood up, too surprised to say anything. "Are you okay?" she asked.

'Eh?' Naruto thought as he slowly opened his eyes, and looked at her. She was a little smaller than him, her hair was pink, which surprised him, she wore a green long sleeved shirt, with tan cargo shorts, that stopped just below her knees. 'She's cute." He thought as he looked at her face, a small blush flashed across it. The last thing he noticed were he striking green eyes, he gave her a wide grin.

"Hehe, I'm fine, more importantly, I didn't know hurt you when I knocked you over did I?" He asked.

"Um, I'm fine thanks" She replied, shocked when he replied in that serious tone. She looked him over, he was wearing a white t-shirt with what looked like an orange spiral on it and a pair of khaki coloured shorts. She looked into his eyes, 'His eyes seem they like they're staring right through me, there's something about them, I wonder what it is?' She thought, she glanced at the rest of his face, 'He's also quite good looking', she blushed soon after fully realizing what she'd thought.

"Stay away from him girl, he's dangerous" an elderly woman spoke as she walked by, hearing their conversation.

Naruto looked down, as Sakura seemed to frown at the older woman, she noticed what he'd done and eyed him curiously. He felt her eyes on him, and quickly looked up to face her, he gave a sad smile before telling her he'd see her around. He walked off.

About 10 steps later, he heard "Wait! Wait please!", he turned around to see who it was, surprised to find the girl he'd just bumped into.

"Hey! Don't just walk off!, What was with that old lady back there? In fact, you keep getting nasty looks and some particularly horrible comments from the villagers, even in broad daylight, did you do something wrong?" She asked innocently. Naruto thought about what she said;

'She seems nice, I wonder how she'd react if I told her about the Kyuubi, maybe I should start being more open about it, and see what happens.' Naruto thought.

"I've got to go, but I'll tell about me later on today, meet me on the top of the Hokage monument in 3 hours time okay?" Naruto asked.

"Uhm, okay, oh, what's your name?" Sakura replied, curious as to whom the mysterious boy in front of her was.

Naruto thought for a moment before telling her; "My name's Uzumaki Naruto! Remember it, because you're going to be hearing it a whole lot from now on!" He laughed after he said it, and surprisingly she giggled slightly as well.

"Well, my name's Haruno Sakura" She promptly replied, smiling as she did so.

"Ok, Sakura, don't forget, top of the Hokage monument in 3 hours, I'm already excited". He shouted, running away from her with a skip in his step. 'He's so odd' she thought as she walked back home.

Sakura opened the front door of her and shouted "I'm home!", she took off her shoes and stepped into the open plan hall of her house.

"I'm in the kitchen dear" her Mother replied. Within a matter of seconds, Sakura walked into the kitchen and sat down on a stool, swinging her legs.

Yori smiled at her daughter, catching her entrance out of the corner of her eye, she turned to face her with a smile on her face, she noticed Sakura's face had a thoughtful expression.

"Something wrong dear?" She queried.

Yori had already turned back to preparing dinner when Sakura asked her question.

"Okaasan, do you know about Uzumaki Naruto?" Sakura asked, wanting to find out anything she could about mysterious boy she'd met earlier.

Yori froze upon hearing her daughter's question. "I know of him, why do you ask?" Yori responded, caution evident in her voice. She'd decided that if Sakura ever met the boy, she'd let her form her own opinion about him, Yori herself thought the boy was a hero. She was disappointed at the rest of the Village's treatment of him.

"I bumped into him earlier today, he was getting all these nasty looks from people and horrible things were shouted at him, he was nice to me and asked me if I was okay after he knocked me over, do you know why he's treated that way? Oh yea, he also told me to go and meet on the top of the Hokage Monument in 3 hours, is it okay if I go, he said he had a secret to tell me." Sakura replied, a sad tone noticeable in her voice.

Yori smiled, she liked the fact her daughter didn't just brush off the comments, she knew Naruto was a prankster, and that might have convinced the children the comments were justified. She was proud of her daughter for at being so observant, and also for not running off, which she tended to do when meeting new people on her own.

"Of course you can go and meet him, dear, I do know why he's treated that way, but it's up to him to tell you about it. Who knows? That could be what he's going to tell you later." Yori laughed as she finished her sentence and turned back to slicing the vegetables.

Sakura thought about what her Mother had said, and decided it was best to respect Naruto's privacy and allow him to tell her whatever it was when he was ready.

"Hai, I understand, I'm going to my room." Sakura said, leaving the room and going upstairs.'

2 and a half hours later:

Naruto had spent the last 2 and a half hours, eating ramen and discussing meaningless topics with Teuchi and his daughter Ayame, they seemed to like him for who he is, and didn't even care about the Kyuubi that was sealed inside him, it gave him some satisfaction that there are decent human beings in the world, his encounter with Sakura earlier in the day only seemed to strengthen that possibility.

He slowly made his way to where he had asked Sakura to meet him earlier, he reached the top of the monument and sat down, taking in the beauty of the village from, what he said, the best view ever.

Sakura made her way slowly towards the Hokage monument, thinking about various things that Naruto could say, had he pulled some unspeakable prank that he can't let anyone know about, was he related to someone who'd done terrible things, many thoughts of this kind rushed through her head as she finally reached the top of the staircase, and noticed a blonde head of hair in the distance. She smiled when she noticed him, she didn't know why.

"Naruto!" She shouted as she walked up to him.

Naruto heard her voice, so he stood up and turned towards her, "Hi, Sakura-chan", he noticed a faint frown appear on face, before a blush crept up after it, 'Have I done something wrong' He thought to himself.

"I – I'm sorry, Sakura, I haven't really spoken to many people my age, so I don't really know how to speak to you", he laughed as he finished his sentence.

Truth be told, she didn't him calling her that, the only reason she frowned was because she unsure of how to react, no-one had ever called her anything like that before. She frowned simply because she was shocked, the blush however was unexpected and she couldn't explain it.

"Let's sit down" Naruto offered , Sakura nodded and sat down next to him, before glancing out over the village.

"Wow, this view is amazing" she said, only for Naruto to laugh and agree.

"Yea, I come up here quite a lot, just to look out and think about lots of things." He told her. "Anyway, I've got something important to tell you".

This caught her attention so she remained quiet while he continued.

"You know tomorrow is October 10th right?" She nodded, looking slightly confused, he chuckled before continuing, "You know about the Kyuubi attack and Yondaime defeating it at the cost of his own life?" She nodded once more.

"Well, that's not exactly true." He didn't even bother looking at her, he could just feel the confusion radiating off of her. "You see, tomorrow is my birthday." He turned to face her now, she looked shocked. "Now listen to me carefully Sakura, you can't reveal what I'm about to tell you to anyone, do you understand?" She nodded her head furiously, as if demanding to be told what the secret was immediately. "Right, well the Kyuubi is sealed inside me, and the villagers know this, so that's why you see them calling me names and giving me nasty looks in the street." Sakura's eyes were widened now, she felt shock and disgust at the villagers' course through her veins, and she couldn't help but start sobbing a little. This surprised Naruto who immediately tried to comfort her.

"He – hey, don't start crying on me now" He joked. She looked up from staring a hole in the ground to a smiling Naruto. "Listen to me, I don't mind it, I'm used to it now, as soon as one of them let slip I was the Kyuubi. I got worried and went to speak to Jii-san, oh I mean Hokage-sama, about it, he told me that the Kyuubi should be affecting me somehow, but something has prevented it, he doesn't have any idea what is, neither does Kakashi-niisan or Jiraiya, he's some legendary ninja apparently, but all I've ever seen him do is peek on women in the hot springs."

Sakura went pale at this and eyed him suspiciously.

Naruto was confused for a moment before suddenly catching on. "WHAT!? No! I didn't join him or anything, I tried my hardest to stop him, but I couldn't do anything, so I had Jii-san come down and discipline him." He laughed for a bit after that, before regaining his composure and continuing.

"He said I should have some kind of markings or indication I'm a Jinzuuriki, I think that's what he called it, oh wait no, it's Jinchuuriki, it means something like "The Power of Human Sacrifice", I'm supposed to protect the village against the Kyuubi and be viewed as some kind of hero." He stopped abruptly and gazed out over the village, before laughing to himself. "At least that's what Yondaime wanted me to be seen as". He smiled sadly as he continued staring out across the village. "But since I don't have any markings, I'm not recognized as easily as I should be; I suppose I should consider it a blessing, as to what some of these villagers have done to me." He spat out, venom dripping off every word. Sakura frowned at this, thinking about some of the words she'd heard people use against Naruto earlier today; she sobbed a little harder thinking that was something he had to go through every day.

He placed his hand on hers unconsciously, she was surprised by this gesture and asked him; "But why did the Yondaime choose you?"

Naruto shook his head, and told her "I don't know, Jii-san won't tell me, I think it's because I was just a newborn orphan since I've been told my mother died during child birth, I don't know about my father, I guess he died before I was born, or he left my mother when she was pregnant. I don't really think about them."

Sakura squeezed his hand in response and stood up, releasing Naruto's hand in the process. She looked down at him and smiled, before telling him; "Naruto, thank you for telling me about yourself, maybe tomorrow we can have a party for your birthday?"

Naruto was shocked; someone finally wanted to have a birthday party with him? He stood up and rubbed the back of his head sheepishly. "I don't know Sakura-chan, I haven't got any money so we couldn't do anything, since we're both still young we can't work either so I have no income apart from what Jii-san gives me occasionally and sometimes even that isn't enough." Naruto told her.

Sakura just smiled at this, "Don't worry, we don't have to go anywhere, we could just spend the day together and have fun." She replied.

Naruto seemed to like this idea and quickly regained his former confidence, "Yeah! It'll be fun" he shouted, grinning widely, which in turn got a small happy smile from her.

Flashback End.

"Well, no use sitting around here, I may as well go and find him" Sakura thought aloud. She stood up and walked out of her room and down the stairs. "Mum, I'm going out!", she shouted into the kitchen as she was putting her shoes in, "Ok dear, be sure to back in time for dinner", Yori shouted back to her daughter. Sakura just smiled and responded with a quick "Hai", before walking out the door.

Back with Naruto:

Naruto was currently lying on the ground crying in pain as villager and ninja alike continued to kick and stamp on him.

"WHAT IS GOING ON HERE?!" A roar echoed around the area, freezing all in the place, the mob turned to see a furious Hokage and a group of ANBU by his side.

"We're punishing the demon, Hokage-sama!" one of the more confident members of the mob shouted out.

The Hokage stepped forward causing everyone in the area to unconsciously step back, "A demon you say? All I see is a 9 year old boy, that you're abusing I might hasten to add, I've told a few of you here once before, that neither Jiraiya nor myself, can find any trace of the Kyuubi's chakra within his body, so your excuses of 'It's the demon in disguise' will never work". The Hokage furiously told them.

Some of the weaker minded villagers began to realize what they've gotten themselves into, and gulped.

"Frankly, I don't know if there's anyone stronger in the village than me or Jiraiya, so whoever decided to beat the boy this time, step forward now." The Hokage commanded. A Chuunin stepped forward proudly, ignoring whispers "You fool, what are you doing?!" and "Imbecile.". The Hokage walked towards the man, everyone in the area expecting him to do something, only for him to ignore the man and walk over to Naruto.

"Naruto, are you alright" Hiruzen asked softly. Naruto looked up towards the man, and nodded, before allowing himself to fall into unconsciousness. The Hokage smiled at this before picking the boy and carrying him past the Chuunin, noticing the glare the Chuunin gave him. He reached the group of ANBU, and said, without even turning his back; "Take this fool to Ibiki and have him killed afterwards, considering what they've done to the boy this time, I should do far worse but I don't want to risk incurring the wrath of the council."

Two members of the ANBU seemingly disappeared and suddenly reappeared behind the Chuunin and swiftly chopped him across the back of the neck. One of the them slung the offender over his shoulder and shunshinned out of the area. The Hokage turned around and faced the group, a look on his face that none of the group had ever seen before. "I suggest you leave this area within the next five seconds, if you don't want the same fate as your so-called leader." He told them. It didn't take a genius to realize he was deadly serious and the entire group had dispersed before the 5 seconds had even passed.

"I'll take him to the hospital, I want you to get me the names of any of the ninja you recognized in that group, and have their names on my desk within the next 2 hours" The Hokage spoke.

The remaining ANBU members simply nodded before shunshinning away. The Hokage sighed; looking down at the boy he smiled and proceeded towards the Hospital.

The Hospital:

A Doctor sat in the staff room with a cup of coffee resting between his hands. The door suddenly burst upon and a Nurse frantically looked around the room, before her saw the Doctor.

"Izashi-san, Hokage-sama has brought Uzumaki Naruto in again, he looks to be quite bad this time as well." The Nurse told him.

"What?! Shit, not again!" Izashi stood up, the coffee slipping out of his hands in the process, rushing out the door with the nurse, "Which room are they in?" He demanded, a tone in his voice the Nurse had never heard before.

"205." She replied, he nodded before rushing off ahead of her, "Thanks, now find another Doctor, if it's as bad as I think, we're going to need them." He shouted back.

She merely nodded, before turning back the way she came, looking around for anyone she thought looked qualified enough to deal with the Uzumaki boy.

Room 205:

"I came as soon as I was told Hokage-sama, how is the boy doing?" Izashi, who had just entered the room asked while keeping his eyes on the sleeping boy in front of him.

The Hokage nodded and replied; "He's fine now, I've had a nurse perform some basic medical jutsu to heal any of his cuts and bruises, he should be free to go within the next few hours, but I called you to ask if you could do a quick scan to make sure there is no internal damage."

Izashi merely nodded before standing next to the bed, performing a few hand seals causing both hands to glow a dull green, placing them on the boy's chest. As he was going through the normal tests of such a scan, he asked the Hokage, "What happened this time Hokage-sama?"

He heard Hiruzen sigh before he told him, "Some imbecile Chuunin decided to lead an attack against the boy, I've had him escorted to Ibiki and he's been sentenced to death. It may seem a bit extreme but I think its fair compared to what Naruto has been subject to throughout his life. I keep reminding people than neither me nor Jiraiya can find any trace of the Kyuubi's chakra in his system, but they still seem adamant, they must think it's masking its chakra or something. It's extremely strange though, he should definitely have some of the Kyuubi's chakra in his network, but there's no trace of it at all, as if it's being held back or perhaps even forced back. I know Naruto already as more Chakra than I do, and he's not even a Genin. I thought it was because of the fox, but once Jiraiya and I did a more intense set of tests on him, we realized that's his normal amount. It's clear to me that Naruto has double if not triple the amount of chakra a Kage would have."

Izashi was shocked at this, "But – but how is that even possible?!" He managed to get out.

Hiruzen smiled and told him "Like I said, I have no idea, I'm sure once he joins the Academy, we'll find out."

An Hour Later:

Sakura had been searching around for Naruto, she'd looked everywhere; his house, the Ichiraku Ramen stand, the markets in case he was out shopping for food other than Ramen, the top of the Hokage Monument, all of these places and there was no sign of him at all.

She started to worry and decide to go and ask the Hokage if he'd seen him.

Hiruzen was currently sitting at his desk, skimming over the vast of amount of paperwork that still needed to be done by the end of the day, he groaned inwardly before picking up a pen and signing the first sheet.

A knocking on the door shook from his signing spree, he looked up before uttering "Come in", he instantly recognized the girl who had entered, Naruto's only friend, Haruno Sakura, he smiled before gesturing her to come and sit down at his desk.

"Hokage-sama, do you know where Naruto is?" Sakura queried.

"Ah" Hiruzen said, Sakura had already noticed the look on his face, one of disappointment and sadness, "Did something happen to him?" She asked, as if demanding an answer.

"He's in the Hospital, he was attacked earlier, and it always gets worse this time of year." Hiruzen responded sadly.

"Oh...I see, well, is he ok and can I go and see him?" Sakura had never gotten used to the fact that Naruto was hospitalised quite often and it always brought tears to her eyes.

Hiruzen smiled fondly at the girls' question, "He's in Room 205 over at the Hospital, he was sleeping when I left, but that was about half an hour ago, I'm sure he'll be awake and happy to see you, go now." He spoke with a smile on his lips.

"Hai, I'll head over there now." Sakura smiled, she stood up and walked out the door, before breaking into a full sprint to reach the Hospital as soon as possible.

Room 205:

Naruto was just waking up; he seemed to ache all over, all he could remember was the crowd beating him and then suddenly stopping.

He stood up out of the bed, almost collapsing from the pain in the back of his leg, 'Oh that's right, that shuriken, I'd forgotten about that', He thought to himself, whilst still trying to regain his footing, he grasped the side of the bed and pushed off towards the windowsill, making a grab for it and pulling himself up.

"Huh, sometimes I wonder about this village, I'd have gotten out of here long ago, if it wasn't for Jii-san, Ero-Sennin, Kakashi-niisan and Sakura." He thought aloud as he looked out across the village.

"What was that about me?" Sakura asked with a smile on her face as she strolled into the room and sat on the other empty bed in the room.

"Ah! Sakura-chan, it was nothing, but what are you doing here?" He asked her as he slowly turned to face.

"I heard from Hokage-sama that you were attacked earlier, so I decided to come and make sure you were ok." She replied sadly.

He turned around at this point, "I'm fine Sakura, really." He responded.

"Hmm, alright, do you mind if I stay here for a bit longer?" She asked him. She know he wasn't alright and there was something he wasn't telling her, she figured it was about the village, but she know not to pry into those matters, without him talking to her about it first.

"Sure, as long as it's you, I don't mind." He grinned widely, which caused her to blush slightly.

"So what are we going to do for your birthday tomorrow?" Sakura asked.

"With the way things have been going this year, probably hiding in the forest outside of Konoha" He joked. "No, I think we should just go to Ichiraku and act like any normal day, the festival for the defeat of the Fox will probably take up almost everyone's time anyway." He spoke seriously this time.

She looked at him and smiled before agreeing. "I'm going to go, you'd best head straight home when you get out, in case some people have already planned something." She advised him.

He nodded before saying Good-bye to her, giving her a wide grin as she left and turning back towards the village.

The Next Day:

Sakura and Naruto had had a surprisingly fun day, considering the circumstances, they had lunch together, and spoke about various things at the top of the Hokage monument, it was later in the evening, and an ominous feeling had crept into the village.

Naruto had realized he had no groceries so he'd gone out to fetch them, on his way home however a large group of drunken villagers and ninja had decided to punish him, their excuse the same as always "This is what Yondaime would have wanted."

Naruto was sprinting away as fast as he could, in his confusion he'd walked into a dead end passageway.

He turned around to hear laughter and sneering comments, he screamed as the crowd set upon him..

The Uchiha Compound:

"Sasuke... Don't come in".

"What?!" Sasuke screamed as he burst through the door, "FATHER! MOTHER!" he shouted as he noticed their bodies on the floor.

"I warned you Sasuke" Itachi spoke as he stepped out from the shadows.

"BROTHER! Father and Mother are dea- ..." Sasuke stopped halfway as his mind registered what had happened.

"YOU KILLED THEM!? Why?!" Sasuke roared as he charged towards his brother, only for Itachi to seemingly faze out of existence and appear before Sasuke, his fist planted in the young boy's stomach.

"You want to know why? Fine, I'll tell you, this clan disgusts me, killing each other over such trivial things, power, authority, it's pathetic. If anything, the last 3 Ninja Wars have shown us that nothing good ever comes from obtaining such things at such a high price, namely thousands of people dead, but this doesn't seem to matter to a clan as fickle as ours, they were planning a coup to take over Konoha, and destroy everything so many people died for." Itachi angrily proclaimed.

Sasuke collapsed on the ground, being violently sick, before running to the door. "DON'T KILL ME PLEASE" he screamed.

Itachi calmly walked up to the boy, grabbing hold of his shirt and turning him around to face him. Before, surprisingly, smiling at him and telling him; "I'm not going to kill you Sasuke, you knew nothing of this, I had hoped I'd be able to make it away without confronting you, I'm leaving the village, to join a group that wants to bring peace to the world, I refuse to stay here. There are only a select few people who I respect in this village, who they are is information I'm not ready to divulge to you yet. Become strong little brother, and when you feel ready, leave the village, I will find you and we shall talk again. Goodbye. I'm sorry."

With that, Itachi struck Sasuke once more in the stomach, causing the boy to topple over unconscious. Itachi was already gone before his body had reached the floor.

Streets of Konoha:

Itachi was currently sprinting along the rooftops of Konoha, 'It should only take another 2 minutes for me to reach the gate, then I can –', He was shook from his thoughts when an enormous chakra spike radiated around the area. 'What on earth was that?!' He decided to trace the chakra back to where it had first come from. He looked down from his vantage point.

"Haha, take that demon!" One of the villagers screamed as they kicked him square in the chest, easily winding him. Naruto had stayed silent throughout the entire ordeal, deciding not to give them any satisfaction. He noticed they parted as a man came forward with an iron pipe in his hands, his eyes widened as he realized the man was going to use it on him. The man stepped forward with a smile on his face, and was about to bring the pipe down onto Naruto's legs when he felt something throw him back, his eyes widened as he coughed up blood, feeling his ribs shatter inside his chest, as he was flung back and into a wall, he looked up briefly to notice the entire group he was with had also been launched backwards, there were corpses everywhere, their arms and legs snapped in grotesque ways. He died a moment later.

Itachi, who had been watching the ordeal, was about to intervene when he saw the man raise the pipe above his head, when he suddenly felt himself being pushed backwards by an unknown force, he had recovered quickly and gone to down to street level to survey the carnage, he was shocked by what he saw;

A small crater laid in the centre of the street with Naruto lying in it, looking around dumbstruck by what had just happened. Itachi walked over to the boy. "Naruto-kun are you alri-?" Itachi was about to ask him if he was alright when he caught sight of the boy's eyes.

'What is this?! This is impossible!' He thought 'That ripple like pattern, I've heard stories about it from scrolls in the Library, I thought it was a myth?! They were supposedly possessed by the Rikudou Sennin, God of Shinobi! The Rinnegan! This boy, who exactly is he?!' Itachi was shocked by this new discovery.

Naruto looked around, his vision was strange, he could see chakra, or at least that's what he thought it was, if he focused enough he could see behind him, he noticed there was someone standing in front of him and he held his hands up to defend himself. "Please don't hit me again!" He had finally cracked, seeing what he'd just done.

Itachi smiled at the boy. "Naruto-kun, I'm not going to hurt you, I have a feeling the people who you killed families might though" Itachi thought about what he was going to ask the boy next and wondered if it was ok. 'He's got the eyes of God, I'm sure they'll let him join, he's not welcome here in this village anyway, ignorant fools'. "I'm leaving the village, would you like to join me Naruto-kun?" Itachi asked.

To say the least, Naruto was shocked by what this man was asking him, he was also curious as to how he knew his name but that would come later, he thought about what the man offered. 'Leaving the village? I'm not exactly welcome here but still, what about Kakashi, Jii-san, Ero-Sennin and Sakura-chan, I don't want to leave them especially Sakura.'

"Will I be able to come back and visit?" Naruto innocently asked. Itachi smiled at the boy "I'm sure in a few years time, you'll be back" He answered. "Can I bring someone else with me? She's my only friend, and she doesn't really like the villagers either, some people have bullied her before, can I go and ask?" Naruto didn't really understand what was going on.

Itachi thought about this. 'There'll be another member; this girl may prove useful over time. They asked me anyway, I'm sure they'll accept Naruto-kun and his friend.'

Itachi looked Naruto dead in the eye, before telling he could go and ask her.

"Meet me at the North Gate in 10 minutes; if you aren't there, I'm leaving without you." Itachi said sternly, making Naruto nod his head furiously.

Itachi sped off to the North Gate, he decided while he was waiting he'd write some letters to the Hokage and Danzo respectively.

Naruto had already reached Sakura's house by the time Itachi had reached the North gate. He was currently standing underneath her window, throwing pebbles at her window.

"Hey, Sakura-chan, wake up!" He shouted. "Urgh, eh? Naruto? What do you want?" Sakura asked as she rubbed the sleep from her eyes, before she could ask him again, he'd already jumped up through her window and landed behind her, "Eh?! Naruto, how did you do that?! We're not even ninjas" It was at this point she noticed his eyes.

"Naruto, what's wrong with your eyes?" She asked him. Naruto smiled.

"I don't know but ever since I was attacked earlier, I feel great, like I can do anything. I was out shopping when this group of guys attacked me, one of them was about to hit me with an iron pipe and suddenly they all launched backwards and then I could see chakra, at least I think that's what it is, although I think I killed those men, but they deserved it! I noticed some of them were the ones who'd attacked me before" He replied simply as if nothing was wrong.

Sakura was shocked, 'Naruto killed someone? This is very serious' she thought.

"Sakura, I want you to leave the village with me" Naruto spoke in a serious tone that slightly frightened Sakura, "YOU WANT ME TO WHAT?!" Sakura shouted. "Shh, shh, listen to me please, I don't have much love for this village after what they've put me through, you, Kakashi, Jii-san and Ero-Sennin, are the only people important to me, without you by my side, I'd have most likely gone insane." He told her. She unconsciously blushed when he finished speaking, "Please make your decision, I have to be at the North gate in about 7 minutes" He said.

'But what about my mother? Actually I'm quite sure she'd be able to take care of herself, leaving the village though? Can I really do that, maybe if I go with them I'll be able to become strong and come and visit my mother and Ino again, show her how strong I really am! Me and Naruto have become almost inseparable this past year, can I really live without him anymore?' She thought, blushing wildly, realizing what she'd thought.

"Alright Naruto, I'll come with you, just let me write something down." Sakura told him. She wrote a quick letter telling her mother she loved her and mentioned Ino, telling her she'll be back to show how strong she's become.

"Alright! Let's go Sakura-chan" Naruto shouted, while jumping out the window with Sakura in his arms and began running towards the North Gate, she was laughing with him all the way.

At the North Gate:

Itachi was standing there, waiting for Naruto, he knew the boy would come, and his hopes were confirmed when Naruto came running around the corner with a pink haired girl in his arms. He skidded to a halt in front of him.

"Alright, let's go going." Naruto said. Sakura looked at the man, "Naruto, who is this?" She asked.

"Oh! Forgive me, my name is Uchiha Itachi, I'll explain to you my reasons for leaving the village as soon as I know we're safe, now follow me" He said before launching into the trees, Naruto following closely behind, easily keeping up with him.

'Just what else can those eyes do?' Itachi thought to himself as he remembered the directions of the map he'd been given, telling him how to reach Amegakure from Konoha.

4 hours later:

"Naruto, let's stop for a little bit, I think we're far enough away from Konoha to stop without needing a constant look out, I'd also like to ask you some questions, if that's ok?" Itachi asked.

Naruto stopped, looking down noticing Sakura had fallen asleep in his arms, he smiled at this, before helping Itachi find a clearing where they could rest for the night.

"What supplies did you bring?" Itachi asked him. Naruto looked up, and blushed with embarrassment. "Uh, supplies, I didn't bring anything" he rubbed the back of his head sheepishly.

Itachi looked at him for a moment. "So be it, go and gather some firewood, I'll lay out my sleeping bag, so your friend can sleep comfortably."

"Oh, her name's Sakura, I'm sure she won't mind you calling her it." Naruto spoke before smiling, setting Sakura down on the ground and running off into the undergrowth.

Within five minutes, Naruto had returned with some reasonably sized branches that looked like he'd snapped them in half, and plenty of smaller twigs. Itachi was quite impressed by this. "Naruto, how did you know exactly what kind of things to collect?" He inquired.

"Oh, I went to the library and read a lot about Ninjas, I was going to enrol in the academy the day I turned 10, so I could prove to the villagers that I want to help them, not destroy them as they always seem to think" He replied sadly.

"I understand" Itachi replied. "Now I want to talk you both about something important, would you mind waking, uh, Sakura was it, up for me?"

Naruto complied and shook Sakura awake. Giving her a few moments to regain her bearings and rub the sleep out of her eyes, he continued.

"Naruto, do you feel any different since what happened in the street?" Itachi questioned. Naruto took a few moments before answering, "Yeah, I feel great, but my eyesight has become all strange and distorted, I think I can see chakra. It looks odd, inside your body I can see these strange lines, do you have any idea of what they are?" Naruto finished with a question.

"I have some idea of what you can see Naruto, do you see them randomly around the body or do they follow a set course? Such as up and down the arms, also on these paths, do you see small circles every so often?" Itachi asked.

Naruto looked at Itachi for a moment, before answering, "I see the lines go up and down your arms, there are also the small circles you mentioned, and it looks blue."

'I thought so' Itachi thought. "Naruto, you can see the Chakra pathways, the things that allow chakra to travel around the body, they are veins for chakra, to put it simply. The circles I mentioned are called Tenketsu; they can limit the amount of chakra that flows around the body and if manipulated by the correct application of force, can be closed off completely, blocking the flow of chakra. I also want you to take a look at this." Itachi said as he handed Naruto his forehead protector. "Look at your reflection."

Naruto did as he was told and almost collapsed. "What's happened to my eyes?!" He roared.

Itachi smirked before speaking, "It's called the Rinnegan Naruto, it's a legendary Doujutsu, said to be possessed by the man who discovered the true use of chakra and invented Ninjutsu, The Rikudou Sennin. I don't know anything about it apart from the thing we've just learnt, that you can see chakra. I'd also like to check something out when you've calmed down a bit more."

Naruto was currently staring at his reflection on the forehead protector; he gradually began to accept the way he looked, before moving the forehead protector closer to his eyes. 'Hey, they look pretty cool' He thought to himself.

Sakura was sat there absorbing all the information Itachi had just told them, she took a closer look at Naruto's eyes now she'd woken up properly, 'Wow, they look amazing, I've never heard of anything like this before, his eyes have changed completely, the whites of his eyes are gone, I wonder what those circles are though' She thought as she gazed into his, now silver coloured, eyes.

"Right, let me get this straight, I have a legendary Doujutsu, called the Rinnegan?" Itachi merely nodded, "It was said to be possessed by the man who invented Ninjutsu?" Itachi nodded once again, "Well, I've got to say, THAT'S AWESOME" Naruto shouted as he started laughing, Sakura started laughing as well. Itachi had a slight unnoticeable smile on his face.

"It's quite ironic really, a boy who was constantly beaten and ostracized for something that was out of his control, will likely become one of the strongest ninja of all time." Itachi stated matter-of-factly.

Naruto and Sakura stopped laughing after they heard what Itachi had just said, and just sat there for a few moments their mouths open wide, this caused Itachi to smirk and added, "Even if I reach my full potential, if you Naruto are to reach yours, I will not be able to defeat you, I doubt anyone in the world will be able to stand against you, however, don't think this will just fall in your lap, you will have to train for many years to achieve that level."

Naruto merely nodded before remembering what Itachi had said earlier, "What is it you wanted to check out, Itachi?" he asked.

"Oh yes, I just wanted to see if your new eyes could detect Barrier jutsu as that will be extremely effective if you are sent on Reconnaissance missions. Step back a few feet and let me use one, tell me if you noticed anything different." Itachi said.

Naruto nodded and stepped back.

"Kekkai: Tengai Hōjin" Itachi shouted after performing a few hand seals.

Naruto noticed it immediately, "I can see it, it's some sort of dome surrounding you."

Itachi was surprised, "I see, so you can see Barriers as well? That's interesting."

Naruto just smiled before sitting down again.

"Oh yea, Itachi, why were you leaving the village?" Naruto asked.

Both Sakura and Naruto noticed Itachi flinch at the question before he settled down on a log, and gave his answer.

"I wiped out the Uchiha clan" He replied simply.

Naruto and Sakura were shocked at this, thinking they'd have to force it out of him.

"They were planning a coup, and were attempting to take over Konoha, if they went ahead and did that, other countries would most likely get involved and attack Konoha without warning or repercussion. You haven't seen war, you don't know what it's like to see hundreds of people dead around you, it's terrifying. I did what I had to, to prevent a disaster." Itachi told them.

"I did however, leave my younger brother Sasuke alive, he will join the organization we're going to when he feels he is ready, he knows of the coup, it'll be up to him whether or not he accepts it, if he doesn't and decides to hunt me down, I'll kill him." He added before beginning to pack up his supplies and putting out the fire.

"Come, we have at least another day of travelling ahead of us, we've wasted enough time as it is." Itachi said as he slung his backpack over his shoulders.

They both nodded before standing up and dusting themselves down. Naruto walked over to Sakura and got down on one knee, inviting her to get onto his back, she accepted and within moments, the trio were off, shooting through the trees at an insane pace.

The Next Morning, in Konoha:

"Hokage-sama! Something terrible has happened" A Chuunin rushed into his office.

"Yes, I already know about the Uchiha massacre, I also know that he's taken Uzumaki Naruto and Haruno Sakura with him, leave me" Hiruzen replied without even turning toward the person who'd entered his office.

"Huh, so it's true then" A voice from outside the window called out.

"Yes, apparently the villagers decided to attack Naruto yesterday evening, Naruto killed them and joined Itachi. I don't know how Sakura got wrapped up in all this, but I presume it's because she's Naruto's best and only friend, I have a feeling she went with them willingly, besides Naruto isn't the kind of person to kidnap someone he's so close to." Hiruzen answered the voice.

Jiraiya then jumped up and landed on the windowsill, "He killed them you say? Was it the Kyuubi?" He asked Hiruzen.

Hiruzen shook his head, "No, they were killed by some kind of technique I've never seen before, it seemed like their organs were pushed back, the force must have been immense since all of their ribcages are shattered and there are several bodies with severally broken bones."

Jiraiya's ears perked up at this. "I see, would you mind if I had a look at the bodies? That description reminded me of something I've seen once before." Jiraiya asked.

Hiruzen merely nodded his head, before handing Jiraiya an access pass to the Hospital Morgue.

"I'll speak to you about it later." Jiraiya said before jumping out of the window and making his way towards the Hospital.

Morgue:

"This – this is exactly the same as before! The bruising on the chest, the organs scattered around the chest cavity like someone's taken them all out and put them back in however they please. Well, Uzumaki Naruto, you certainly are an interesting child, I look forward to our next meeting." Jiraiya said to himself as he walked out of the Hospital, heading towards the Hokage tower to report his findings.

Hospital:

Meanwhile in a private room, Uchiha Sasuke was lying in his bed thinking about his brother had said; 'They were planning a coup? Why would they do something like that? We were the strongest clan in Konoha! Now that I think about it, Father had been acting rather distant lately, and Itachi was acting strange as well...Itachi, he theoretically saved my life, I need to think about this more'. He sighed before lying down and dozing off.

Near Amegakure:

"Ok, we're nearly there" Itachi spoke; he could barely be heard over the sound of the pouring rain.

"The sooner we get there, the better" Naruto grumbled, making Sakura laugh.

Amegakure:

"Eh?!" A voice shouted out.

"What is it?" A gentle female voice asked.

"There are 3 Intruders, one of them is Itachi, another is nothing to worry about, but the last, their chakra is almost double mine!" The voice replied.

"What?! How is that possible?" The female voice asked worriedly.

"I don't know, Konan, go and meet Itachi, it seems they all entered the village at the same time, so once you find him, I'm sure you'll encounter the other two." The voice told her.

"Hai, Nagato". Konan replied.

"Be careful" He warned as she was making her way out.

She merely nodded.

Entrance to Amegakure:

"Halt! What is your business here?" The Gate guard questioned.

"My name is Uchiha Itachi, these people next to me are my travelling companions, we seek entry into your village, our reasons are our own." Itachi replied.

"You will state your reasons for being here, or you will be treated as an intru-" The Gate guard had already raised a Kunai to defend himself.

"Stand down, Masuyo, leave them to me" A woman had appeared behind him.

"A – Ah, Konan-sama, I will do as you say! Forgive me!" He bowed his head quickly before returning back to his post.

"My name is Konan, I am an emissary for the leader of this village, state your business." Konan told them firmly.

"My name is Uchiha Itachi, your leader is expecting me, these two people here are my travelling companions, and I request they be allowed in as well." Itachi told her.

Konan knew of Itachi's arrival, she just had to confirm it was him. She glanced down at the two children at his side. She cast her eyes to Sakura, who gave her a quick smile; she had to stop herself from smiling back. She then took a glance at the other boy; he had his head turned around as he was looking around the village. She could feel power radiating off him; she cleared her throat to gain his attention. He turned towards her and she froze on the spot.

'What!? This cannot be, he's got the same eyes as Nagato! I see, this is the chakra he was talking about, he'll be a worthy addition to Akatsuki, perhaps even stronger than Nagato.' She thought to herself.

He grinned at her and said "Hey, my name's Uzumaki Naruto, nice to meet you!"

She suddenly felt a faint smile tug at her lips, before she pushed it to the back of her mind and dropped back into her serious demeanour.

"Hai, now come with me, I'm sure our leader will want to meet and greet you all personally." She stated.

She nodded to Masuyo, and he responded, allowing the three of them passage and recording their names within the journal on the desk in front of him.

They walked through the gates into the city of Amegakure itself. All three of them were taken aback by how the city looked, although only two of them showed a surprised looked upon their faces. Itachi remained stoic as ever.

"Whoa, this place is amazing" Naruto spoke, voice filled with awe as he glanced upwards, his sight filled with towering skyscrapers.

Sakura could only nod, too taken aback seeing a city like this.

It was at this time; Naruto had cast his gaze upon Konan, and noticed what she was wearing.

"Hey, Konan-san, I like your cloak" He said. She just carried on walking; none of them could see the faint smile on her face.

They continued on through the city, with Naruto making stupid remarks almost constantly throughout the short journey.

They soon reached the entrance to the highest tower in the city and Konan stopped abruptly in front of it.

She turned and spoke to them: "We're here, through this door lies your future, are you willing to proceed?"

She was surprised by how quickly all three of them responded. Satisfied with the three nods, she gathered some chakra into her hand, and placed it across the barrier in front of the door. Once the barrier had finished dispersing, the doors opened themselves and they all stepped inside.

They walked into a strange foyer, noticing there was no-one there, they passed through it and walked up the stairway on the other side. Reaching the top of the stairs, they stepped out onto a balcony, noticing a figure standing in front of them, leaning over the balcony railing, observing the village.

"Greetings Itachi, I see you've decided to join us after all." The man spoke. Itachi replied with a swift "Hai".

"But it seems you've brought along some stragglers." He said.

"Hey!" Naruto shouted out, only for Itachi to grab his shoulder, turning him around to face him and shaking his head, Naruto soon quietened down.

"They will become strong and valuable members; that I can assure you." Itachi replied.

"Yes, I can sense that boy's chakra; it's stronger than any I've ever felt before, even my own. The girl's, while not as strong, is still fairly potent." He continued whilst still looking out across the village. "But have you ever felt pain before? Do you know what it's like to feel like the whole world is against you, having everything you've ever loved brutally torn away from you, in front of your very eyes?" He asked. This time he turned around. "Do you know what it's like t-". He stopped dead as he opened his eyes and caught sight of Naruto.

"...What? This cannot be." He spoke quietly.

"Hey, your eyes look like mine!" Naruto shouted.

'This boy, his eyes are the same as mine, yet he possesses almost twice my chakra, this is impossible, yet I'm staring right at him.' Nagato thought to himself.

"What are your names?" He asked them.

"Uzumaki Naruto." "Haruno Sakura." They each replied.

"I see." He thought about what he was about to say for a moment, "Very well, Konan, take them to an empty room, I shall be along once I've conversed with Itachi." He said.

Konan merely nodded while gesturing for Naruto and Sakura to follow her.

As they walked out of the room, Pain turned back towards the village.

"I see now why you brought them with you, that boy has the Rinnegan, it was a wise move." He spoke.

Itachi nodded once before speaking. "You should know something else; he's the Jinchuuriki of the Kyuubi." This caused Pain to freeze before turning to Itachi, gesturing for him to continue, "But as I'm sure you've noticed his chakra pathways haven't adapted to the Kyuubi's chakra, it seems to me, that the Rinnegan has suppressed it's influence. You could theoretically remove the Kyuubi from him, without killing him in the process as his body doesn't rely on it." Itachi continued. "As for pain, he was beaten daily in Konoha, his apartment needlessly vandalized, there were a select few who appreciated him, I'm sure you know of them. It was Sarutobi Hiruzen, Hatake Kakashi and Jiraiya. The rest of the village is most likely celebrating his departure." Itachi finished.

"I...see" Pain replied. "He will be a fine ninja, I will have to oversee his training here though, the Rinnegan will crush him if he's not prepared for it. I shall introduce him and yourself to the rest of the members tomorrow; I have a plan that will require all of you." He stopped, seemingly thinking. He turned back to face Itachi before continuing, "What of the girl?"

Itachi didn't take long before answering, "She is Naruto's closest, if not, only friend. He asked me if she could come, I agreed. She seems very intelligent; I suspect in the future, they will become a force to be reckoned with."

"Very well, I will have Konan teach her, she shall become a medic Nin, what else Konan teaches her will be her decision." Pain said.

"Now, I'm sure you'd like to get some rest from your journey, Konoha will never think to look here, so you're safe for the time being." Pain spoke, Itachi merely nodded before following him out of the room; they soon reached a door. "You can stay in here for now." He said, before walking off, leaving Itachi outside the room.

Naruto and Sakura were each sitting on their new beds, with Konan standing by the door, watching them. The door opened and Pain stepped through. He glanced at Konan, before stepping in the room fully, and speaking to Naruto. "Naruto, I would like to speak to you about something, it's important, would you like this girl to stay or leave?" He asked.

"She can stay" Naruto answered firmly.

"So be it. I'm going to tell you about those eyes of yours, as Itachi has most likely already told you, they are called the Rinnegan, and were possessed by the so-called God of Shinobi, The Rikudou Sennin." Naruto merely nodded, before Pain continued. "What he most likely didn't tell you are the benefits of having such eyes; first, you possess all six of the Chakra elements, allowing you to perform almost any technique you wish. Second, they provide you with a huge amount of chakra just by awakening them; I won't ask what happened to cause this. However, it seems you had a huge amount of chakra to begin with, so your levels are now the highest I have ever seen." Naruto sat there in silence, taking it all in. "There's something I want to ask you; before you awakened the Rinnegan, did you have any other episodes? Fits of rage where you'd black out and wake up, not being able to remember what had happened?."

Naruto shook his head; "No, this is the first time it's ever happened."

'I see, Itachi was right, there's no trace of the Kyuubi's chakra at all, even on his stomach, where the seal of Jinchuuriki usually is. We may be able to take remove it from him without killing him. It'd be a tremendous waste if he were to die.' Nagato thought.

"I also know you're the container of the Kyuubi." This caused both Naruto and Sakura to visibly flinch. "However, we may be able to remove it from you, normally this would kill you, but it seems like the Rinnegan has suppressed it's influence from birth, therefore your body has not become accustomed to it's chakra, so it's just sitting there inside you. Almost separate from you." Pain finished.

Naruto looked at Sakura, before she nodded slightly, he nodded in return before turning to Pain, "I'd like to risk it, I just want to be seen as me." He said.

"I understand, tomorrow I will introduce you two to the rest of Akatsuki and we shall begin the sealing from there." He then turned to Sakura, "You will be training with Konan here" He said as he gestured to Konan, "in the art of medical ninjutsu, when you two are inaugurated into the organization, you shall be partners, performing assignments and various other tasks I will ask of you."

They both nodded, before Naruto could open his mouth, Pain had already begun answering his question. "Your training Naruto, will consist of me teaching you the various techniques of the Rinnegan, however, I will only teach them to you once I see you can handle them. I'll have the rest of Akatsuki teach you as many elemental techniques as possible, we'll also discuss Taijutsu but all of this will come later. For now, I'm sure you'd like to rest. Come Konan."

Naruto merely nodded before Pain and Konan left the room, leaving him and Sakura alone, Naruto turned to Sakura before saying:

"Well, that was some birthday."

END.

Another quick A/N: Thank you for reading this first chapter! I hope you enjoyed it, if not, well okay.

I know some of the characters are OOC at points, but meh. I really enjoyed writing it.

The next chapter will probably be out in the next few days, if I can be bothered to drag myself off Mass Effect 2.

And yes, I know the Kyuubi thing is cheap, but I just wanted to get it out of the way early on. Sorry and thanks once again!