"No! It wasn't supposed to be this way!"
The Kyuubi roared in anguish as he felt the Yin half of his chakra – the chakra that allowed him to create form from nothingness, the chakra that allowed the fox to wield its immense spiritual powers – be ripped from his soul and then be sealed into the detestable Yondaime Hokage with the assistance of the Death God – a being who only rarely directly intervened in mortal affairs. For an intervention on this scale, the price that the Yondaime would pay would be unfathomable in its cruelty – eternal battle and torment in the Death God's own bleak, desolate realm.
Neither Mito nor Kushina could have ever hoped to be my true Jinchuuriki; my full powers are far too vast to ever be sealed into a mere human. They were merely vessels, incapable of drawing upon my powers! Kushina's husband summoned the Shinigami to separate me from half of my powers…surely in order to weaken me enough to be truly sealed into Kushina's newborn son! Who just happens to have the potential to serve as my first true Jinchuuriki! I will never allow it! I will never again be enslaved! Not by the Juubi, not by humans, not even by the god of death himself!
Kurama roared like the incarnation of the World Chakra that he had once been a part of, and, defeating Kushina's cursed Chakra Chains despite his weakened state, the Fox reached out and attempted to destroy the woman's newborn son. Though the Fox's physical size was, with the loss of its Yin chakra, a mere fraction of what it had been moments ago, the great beast still had enough reach left to accomplish this final murder.
A part of the Fox regretted that it had to be this way. The boy, during his unnaturally long ten-month gestation period, had absorbed a portion of the Fox's chakra – which could regenerate easily enough – and more worryingly, the boy had even absorbed a tiny portion of the Fox's life force, or in other words, a small shard of the Fox's spiritual connection to the World Chakra. This meant that the boy would have had, if he'd had the opportunity to grow up, unparalleled potential as a Sage to sense and draw upon natural chakra, and the chakra of demons and spirits.
The child was the first human in existence born with such a trait. Other children of female Jinchuuriki had commonly absorbed some of their demon's chakra, sometimes manifesting new bloodline limits as a result, but this absorbing of spiritual essence…this was new. It was only made possible with the recent forays that the Uzumaki Clan had been making in the spiritual aspects of the sealing arts – surely the means by which they had learned to directly call upon Death itself. Kushina's seal, the most advanced ever used on a Jinchuuriki, had allowed for unparalleled closeness for Kushina's and Kurama's spirits – and despite that, it still wasn't powerful enough to allow Kushina to even marginally control Kurama. It was just physically and conceptually impossible given Kurama's overwhelming power. Her seal would have more than sufficed to utterly dominate any other demon, but with the Kyuubi, a being normally more powerful than all of the other Eight combined…it was simply impossible.
Kurama felt the satisfying sensation of blood on his meters-long talon.
I got the child! I killed him! Now…to finally destroy Kushina and her husband. If I consume the man's spiritual essence before the Death God departs, I should be able to reclaim my chakra. If not, I should still be able to reclaim my Yin half, though the preparations will take decades. Once they're dead, I will then destroy the village of my cursed enslavement! Then I will destroy the masked man who released me from Kushina – something for which I would have ordinarily granted him unfathomable rewards – and enslaved me, ordering me to do that which I would have done anyway! Then I will reclaim my freedom once and for all!
I will have my revenge on Madara, Hashirama, Mito, and all of the others who denied me my freedom, granted to me by the Sage of Six Paths himself, by my father!
Then Kurama looked down, realizing that Kushina's chains had strengthened, paralyzing him utterly. Seeing what lay before him, he began to know fear.
The child lives!
Kurama saw the cursed Uzumaki woman fearlessly stare him in the eyes, despite her mortal wound. She spoke her final words to her former tenant. She had always had too much stubbornness for her own good…
"Sleep, Kyuubi. Sleep in my son. You will protect him…and he will protect the world from you."
Kurama was helpless. Between Kushina's chakra chains, and the grip of the Death God, he was completely paralyzed. He could only watch and listen as Minato and Kushina imparted their final words to their son, and, with that done, Minato sealed the remainder of his and his wife's chakra into the newborn. With that finished, as Kushina slumped in death, Minato tiredly looked Kurama in the eye and spoke his final words.
"Kyuubi…we humans have never done you any favors." The fox snorted hatefully, causing Minato to quirk his lips into a half-smile even in this final moment of his life. "But, please listen to me. The masked man who took control of you this night, the one who called himself Uchiha Madara…I don't know what he is, but I do know that he is the harbinger of a calamity foretold by prophecy, predicted by the Oracle of Myobokuzan. Please, help my son defeat this evil. Please help him achieve my dream in my place, to bring peace to the Elemental Nations."
Minato's eyes were now deeply hooded. His body felt so cold. The Kyuubi's Yin chakra was so heavy. Minato would be dead in seconds with or without his contract with the Death God. The spiritual half of the Kyuubi's chakra should, according to theory, follow him to that dark realm, forever bound to his soul, forever beyond the Fox's reach.
"Kyuubi…I am sorry that my village has been forced to enslave you. No one should have their freedom stolen, not even you." The Fox's eyes widened in shock. He had never expected this of all possible men to say such a thing to him, to apologize to a tailed beast – especially at this of all moments. Minato chuckled weakly. "You don't owe me any favors, Fox. But, please…help my son…save the world…"
Minato's final sight was the confusion in Kurama's eyes.
Deep within Uzumaki Naruto's spirit, several hours later
For the first time in thousands of years, an entity greater than even the tailed beasts awakened. It possessed only a miniscule fraction of its former sentience, its intelligence. It had never been meant to be woken in this incomplete state, with the vast majority of its spirit still sleeping in its other eight creations. The being had originally been meant to be awoken far into the future in its complete state, when the Nine, which had once been One, became One once more. It was then that the being's nine hidden spiritual fragments would have the opportunity to unite once more and change the world.
However, with the traumatic damage that the Kyuubi had just endured, having half of its chakra permanently stolen by the Death God and being sealed into a new Jinchuuriki, all on the same night, the entity – normally repressed deep underneath Kurama's soul and chakra, had woken in response to the Fox's spiritual agony. Kurama was ignorant to the incomplete being's presence, and would remain so for a very long time. The Fox was now asleep, curling and twitching in agony in a new mindscape, in a new Jinchuuriki's cage. It would be years before the tailed beast awakened.
The half-formed entity looked upon the Fox for the first time in millennia, and seeing its estranged son in pain, it searched for a way to alleviate the agony. It inspected the seal, it inspected this newborn body, and it saw something truly intriguing. This wasn't a normal human body. It had absorbed and incorporated a tiny portion of the Fox's connection to the World Chakra, meaning that this newborn had unprecedented potential to master not only the command of natural chakra, but also possessed the potential to awaken spiritual powers that only two other men in history had achieved.
The half-formed, ethereal entity considered the situation. This newborn was as good a candidate as any that it had ever imagined to reunite the Nine and finally bring peace to the world.
With that decided, the being made a critical alteration to a grand plan that it had set in stone thousands of years ago. The being, momentarily pausing to stroke Kurama's fur, alleviated the Fox's pain, protecting it from the full trauma usually inflicted to newly sealed Bijuu as they acclimated to a new host body and spirit. The entity then faded from Naruto's mindscape, retreating into the deepest possible level of Naruto's soul. There, it began to work changes to Naruto's body and soul, changes that would take over a decade to outwardly manifest – and would in the meanwhile force the newborn to demand unprecedented amounts of raw nutrition.
The being, wreathed in the pure and powerful tabula rasa of the newborn's soul, smiled. It would grant to this child the potential to shake the very foundations of the world, the potential to bring about a true and everlasting peace in an empire extending to the stars themselves. This newborn would be the bearer and final achiever of the entity's dreams.
Meanwhile, in a room of the Hokage Estate
Naruto, wrapped in a blue blanket in the Hokage estate, curled up in his crib and smiled, dreaming of the thing that he would soon learn to call food.
Hiruzen Sarutobi, the priorly retired – and now reinstated – Hokage looked down upon the newborn, with a small smile on his face. The Hokage was still wearing his ancient battle armor, which was now just a little more battered than it had been several hours beforehand.
"Biwako-chan would have loved you, little Naruto."
The Hokage looked to the window overlooking Konoha's central avenue, which had taken horrendous damage several hours before. Thousands of innocents had died on this evening, including the Hokage's own wife. The Third had countless questions and few answers on this evening. Why had Kushina's birth gone wrong? Why had Minato been forced to use the Uzumaki Clan's ultimate sealing technique? Why was Biwako, her medical assistant, and her Anbu guard slain? Who had been the murderer, who was apparently capable of fighting the Yondaime Hokage himself to a standstill? How was he responsible for this attack…this massacre?
Hiruzen, overlooking Konoha's central road, saw a crowd of thousands approaching. They would be asking questions for which the Hokage had no answers. The Hokage thought of his countless memories of his beloved wife, she who had been his life partner for over thirty years…now cruelly taken from him without even a final goodbye.
"Biwako-chan…I need you. How am I going to do this, how am I going to be Hokage again, without you at my side? What am I going to tell Asuma…"
The door opened.
Hiruzen turned around, seeing the mask and white cloak that marked his Anbu General, his second in command of Konoha's military forces.
"Hokage-sama, the Council – the surviving Council – has assembled. They demand your presence…and the child's."
Hiruzen nodded, and then walked back to Naruto's crib, picking the boy up, still swaddled in his blue blanket. The Anbu stayed at his Hokage's side. Mercifully, the child remained contentedly asleep.
Konoha's Anbu General spoke first, looking at the sleeping boy in his Hokage's arms.
"It is amazing to think…that so much power could be contained by one so young, so little."
Hiruzen nodded, as the two exited the room and began to leave the house, dozens of other Anbu assembling behind them in double file.
"Indeed. This child will carry on the dreams of his parents, and he will protect Konoha from the Fox….he will save us all."
Hiruzen looked down upon the sleeping Naruto, cradled in his old but still strong arms. "Naruto-chan, it is time to introduce Konoha to its new hero. Make me proud, child. From this day forth…you are to be Konoha's newest hero…our savior."
This is a story premise that I've always been interested in working on. While there have been others, the intricacies of granting Naruto a Rinnegan without falling into the trap of making him desperately overpowered, thereby cheapening the story, requires a rare talent for writing. I'll be working at this for a while, doing my best...and I hope that you all enjoy it. I intend for this to be epic in length. It's going to be a long ride.
Regarding Kushina's chakra chains, I wanted to write an explanation of them into the actual story, but I didn't see a good opportunity for doing so without it being awkward. I'm envisioning the Chains as a Yang ability of the Seventh Path, the Outer Path, that the most powerful of the Uzumaki, as descendants of the Sage's younger son, could to an extent manipulate. Mito Uzumaki possessed a similar ability – only the Uzumaki with the most powerful life forces, which were nearly always females, could manifest this powerful ability.