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Naruto will have the Rinnegan in this story, but the powers of this unique bloodline have been misunderstood. The most comprehensive understanding that I have had the opportunity to read is here: Naruto Forums search "the powers of the Rinnegan"

I highly recommend everyone read this; he/she has an interesting and well grounded take on this.

If you don't want to, anyways, here is the summary:

Powers of the Rinnegan

1. According to Jiraiya, the Rinnegan allowed Nagato to master all six forms of chakra - presumably the five elements plus one other - perhaps yin/yang.
2. The Rinnegan bestows upon its possessor the ability to see spiritual energy and beings.
- we see Pain observing the spiritual barrier that surrounds Konoha:

- we have Pain being able to see the Hell King Enma with his Rinnegan: This is a being that cannot be detected by anyone else without it interacting with them specifically, much like the Shinigami.

Things That People Like to Pretend Are Gifted by the Rinnegan, but Probably Aren't

1. Jiraiya tells us that, as a child, Nagato expressed an unnatural aptitude for ninjutsu. His hobby was creating and learning new techniques. Given the powers of the Rinnegan, he has an advantage over every other ninja in that regard.

2. Jiraiya does not tell us, however, that Nagato suddenly began manipulating the Six Realms of Metampsychosis.

3. He does not tell us that awakening the Rinnegan granted Nagato access to powers never before seen in the world of ninja.

4. He does not tell us that the Rinnegan comes equipped with a jutsu repertoire as the Mangekyo Sharingan does.

5. In fact, Nagato exhibits no signs of having inherited superhuman powers from his doujutsu in the three years that Jiraiya knows him.

The Six Paths of Pain

Six Paths is NOT a power of the Rinnegan! Full analysis on the link

How does the Sage of the Six Paths come into all of this?
He created ninjutsu, and therefore most likely discovered chakra for what it is, right?

Chakra is a combination of body energy and spiritual energy.

Body energy is sort of obvious here. It's physical fitness and stamina. Any old person could figure this out.

But what about spiritual energy? How do you learn to control something you can't see or feel normally?

Then along came the Sage.

His Rinnegan allowed him to detect the spiritual energy in his body and the bodies around him, allowing him to mold chakra and create the first ninjutsu.

This also helps to explain why Nagato can have so much chakra. Since the Rinnegan is intrinsically linked to spiritual power, Nagato has an immense amount of this energy - possibly more than any other human.

That, or he is simply more efficient in its usage since he is aware of it.

Conclusion

Rinnegan's power is to attune its possessor to spiritual energy and allow him or her to use all six forms of chakra manipulation. Whether this is due to the connection with the spirit or simply a second ability, we can't be sure.

The Six Paths of Pain are not necessarily - nor even likely - a direct manifestation of the Rinnegan's power. More likely they stem from the amazing insight that Nagato has into ninjutsu thanks to his bloodline.

Chapter One

Demon.

Monster.

Animal.

Can't you see we must kill you?

Can't you see you must die for our vindication?

Can't you see they're scared of you?

Run. Run away and don't even dream of coming back.

His muscles involuntary trembled in a futile attempt at generating heat. The funny thing about the rain – the more wet it got, the drier Naruto's sense of humor became. No place; no friends; no identity. He was the void, which absorbed all hatred; the black hole that encompassed all negativity; the black hole whose sole purpose was to prove absolute negativity existed in the Universe.

He understood his place in the world – oh yes, even embraced it. Perhaps if he played the part well enough, he would be reincarnated in the next life as a dog. Yes, a dog with a loving master. That's all he really asked for. Anything was better than this. Anything at all.

Naruto stared at the blade in front of him. Perhaps Kami-sama would smile. Yes, she would grant him peace. A chill smile broke on his face as he felt the familiarity of warmth. Crimson life sped down his arms and splattered stupidly on the ground. The familiar dizziness overcame him as he felt woozy. If only he could die…

"Help me!"

Naruto looked up and saw a little boy desperately hanging onto a small tree branch. With a crack the branch broke, but before the boy met the unforgiving ground Naruto managed to catch him in his arms.

The boy suddenly screamed – as Naruto tried to calm him, the wails only got worse. He pried himself from Naruto's arms and ran to a middle-aged man nearby.

"Do you even know who your father is? You're an accident… No connection whatsoever to this village." The man spat. "How dare you touch my boy?"

Naruto stared blankly at the older male. Then at the boy who offered Naruto a smirk, seemingly satisfied with his work. Naruto realized it was a crude plan to get him in trouble. Suddenly, he weaved through the crowd to dash away, embarrassed at his own misfortunes.

Everyday a similar scenario would occur. Every night he would cry himself asleep, paranoid that someone would find him; that someone would see him and attack him. Make pain come searing through his veins like the last time. That those dark, crimson eyes would make his world go black once more. Yes, death would be far easier… Even preferable.

Naruto jolted when the door inexplicably burst open. Behind them darkness enveloped a cloaked figure, the visage hidden in the mist of the night. But Naruto was all too familiar with this person. This time, Naruto merely smirked. He sardonically gave one last look at the world. Telling fate to fuck itself. He. Didn't. Care. Anymore.

"You're going to kill me." Naruto whispered. It was a statement.

"If I am?" The red eyes began to spin.

"I'm ready…" Naruto floated forward. "Do your worst."

The mysterious man said nothing at this bold move. Perhaps this came unexpectedly. Perhaps he was bidding his time. A wave of apathy washed over Naruto. The futile nature of his existence; the nihilistic dump that he called life. What did it even mean? He didn't care to find out. A kunai came out of Naruto's sleeve. "I'm getting impatient. Are you going to kill me or not?"

A lightning-fast blade whizzed through his heart. Naruto smiled as the recognizable taste of blood flowed into his mouth. The identifiable dizziness as his mind shut down. Death… he had come so close to tasting it so many times before. His wrist gave one last pulsating effort at life before he faded into a comforting darkness.

Alas, that would be too easy. Far too easy. No, his immortal prisoner would never allow that, and true to its word Naruto felt the wound healing almost immediately. He lost everything. The closeness of home – of death. Despondence was new to him – he was always born with nothing. But to have it stripped from him when he was so close… Fate mocked him. He could never die; no matter how much he wished, begged or pleaded. Kami-sama was intent on keeping him a soul-less ghost, forever doomed to walk the earth, merely to seek the afterlife.

A sudden anger surged through his veins. He had not even fallen to the ground before consciousness had forced itself onto him, barging through his mind to assert its dominance. "Pathetic. Aren't you an ANBU? Capable of expertly killing anything?" His eyes glared at the intruder. This imbecile incapable of even properly putting him to sleep. This was all his fault. All of it.

"There are things far worse than death, Naruto-kun." The voice whispered softly, and the eyes changed. "Tsukuyomi."

A blackness devoured him. It was as if everything turned into a grey-scale, only capable of recognizing onyx shades. Naruto had an uncontrollable urge to giggle, and as he succumbed to this innate desire he began laughing manically. "Worse than death? Everything's worse than death. Death is what I've courted for my entire existence. My life has been about seeking death. You – this clever technique that brings me pain… It is but another obstacle that prevents me from actually dying."

The man placed another sword into his body – over and over for what felt like an eternity – and Naruto kept laughing until his throat grew hoarse. The humor of the situation subsided long, long ago. The familiar flames erupted. The entire village. All of it. It must all burn into nothingness. His glare on his adversary intensified, as if his whole being could only see this monster before him. As if… he could see into the very spiritual fibers of his charka. Something began beating on Naruto's head like a drum, but he ignored it; even through the mind-numbing pain, he focused on his only desire: to rip the soul of his opponent thread by thread. To disassemble this chakra-constructed world… To bend this spiritual energy against him… Yes, to take the tip of this sword and slip it into this fool's side… Yes that would be most ideal.

"You? How… How can this be?" The world melted away, fading into reality. Naruto became acutely aware of the blue surrounding this man. He looked at himself, seeing a red core washing over him. 'So that's the source of all these voices…'

That night it seemed even fate had learned to fear him.

N N N N

Naruto packed up his belongings – which did not prove to be a difficult task in the slightest. His apartment consisted of a handful of clothes, an old bed and some books. He left behind all his clothes but a single pair of pajamas – the only set which did not bear any relationship with Konoha. From now on, he was through with this village.

He looked at himself in the mirror for the last time. His eyes had concentric rings around them that alternated between golden and orange. His pupils shone in the darkness. The strangest part was his new ability to manipulate chakra; all of it became suddenly visible to him.

In the dead of night he packed up and bolted. Towards the outer edges of Konoha his eyes saw a massive chakra barrier. He held his hand out and the barrier made a small hole. Passing through, he sealed it quickly. 'They'll probably know… Fuck it.'

N N N N

"WHAT!" Sarutobi stared.

The ANBU stared solemnly, a single abnormally red eye frowning through the mask. "Our troops are unable to locate him, Hokage-sama. His chakra cannot be sensed. Either he has mastered – and I mean mastered – chakra suppression or…" Hatake Kakashi bit his lip.

"Perhaps, Hokage-sama…" another pair of Sharingan stared at him. "There were unanticipated side effects of his attacks. The doctors say he suffered chronic depression."

But Sarutobi was more concerned for a certain nine-tailed demon that lay inside Naruto. There were no signs of anything going awry. The last time it approached the ki could be felt from kilometers away. Today… Today almost seemed peaceful. He sighed.

A third, bandaged man entered the room. "You've done it now, eh Sarutobi?" the man chuckled. "We could have had been be the greatest ninja the Leaf had ever seen. But now?"

"Danzo," The un-retired leader began.

"Two days." A single paper floated to the third hokage's desk. "You have two days to find him before the council proclaims him dead, lifts the ban regarding the Fourth's legacy, and officially re-writes history. Good luck."

'The body… where could the body have gone?' Even his crystal ball was useless in a situation like this.

N N N N

That's chapter one! Thanks for reading! It's much shorter than most chapters