Disclaimer: I don't own Naruto, nor many of the other things I took inspiration from. I write purely for my own enjoyment and don't get any money from this.
Summary: First off, fans of canon Naruto and its themes won't like this story.
This story features an intelligent, independent and fairly powerful Naruto. He might end up in a foursome. It includes politics and intrigue, decade-long plans (that have a tendency to go awry), supernatural powers, gods, ninja fights (later on) and all the human interaction you would expect from a realistically working world. The shinobi world is not a nice place. The build up is very slow, but there will be a lot of changes in Naruto's early life that cause changes of their own, often indirectly. I try to keep the world at least somewhat plausible and logical. Fans of Minato (and to a lesser degree Kushina and the Sandaime) might not like my story, though. Their actions will be viewed in a very negative light as will Konoha's status as a whole (no raving mobs of villagers, but the political and military situation.) and parts of the canon storyline. Many events will happen roughly like in canon, but there will be many changes. If you find the prologue strange I recommend taking a look at the next chapter. It is much more conventional.
Author's note: I recommened listening to the 'Carol of the Old Ones' from the H. P. Lovecraft Historical Society to properly set the mood for this chapter. Simply search for it on Youtube.
Destiny is a Hazy Thing
Look to the sky
way up on high.
There in the night
stars are now right.
Prologue: Old One awakes…
It began. It was. It thought. It was thought.
Knowledge and power were pouring into the fledgling being from some unfathomable source, and it grew. Wispy strands of simple thoughts twisted around each other into more durable, complex cords, which in turn interconnected and formed the many-shaped building blocks of a mind. The blocks sorted themselves into buildings and towers of a structured mind that came crashing down repeatedly when the pressure of even more thoughts and new concepts became too great to bear, only to reform itself into something greater with more intricacy. Individual bubbles of memories hovered above the chaos waiting to connect until the mind had reached a sufficient level to understand them before they too partook in the dance of an emerging consciousness. Finally, the flow slowed to a halt and the mental construct stabilized enough to fulfill its function.
The avatar awoke with a start from its slumber imbued with a single overriding purpose for its existence: assess the situation and act accordingly to ensure its survival. It knew immediately that it was only a specialized part of a far greater entity and that something was very, very wrong. Besides not remembering going to sleep, there was the simple fact that in all its existence the entity had NEVER completely slept. As a matter of fact, it should have been incapable of doing so. Some part of it had to be active at every time, if only to prevent the automatic spontaneous formation of an avatar. Come to think of it, that was exactly what the being currently doing the thinking was. With a feeling akin to dread it spread its awareness inwards, taking in its current status. The avatar itself was made of pure thought and had only some general information and power at its disposal. It was safely encapsulated in its own semi-permeable micro-universe that was otherwise empty. Deep beneath its own familiar if only recently created structure rested the door to the oversoul that connected all separate parts and individual avatars into the greater whole of the entity.
A split off sliver of awareness was send through the door like a sensory organ on a long, flexible eyestalk. At first glance the conduit was almost closed shut from some external pressure that prevented the flow of more power to the avatar. That restricted its possible avenues of actions tremendously. Every action taken, every idea thought consumed some small amount of power that it was unable to replenish. Should it spend all its energy the current avatar of thought would simply vanish. At last the sliver reached the central nexus pool where all things rested that made the entity what is was, waiting to be used to form the avatars that were the entity's equivalent of hands, sensory organs and even brains.
The first impressions it got were smallness, confinement and an all-encompassing feeling of loss.
Where the core of its very being should have stood like a mountain of diamond only a crack-riddled pebble remained.
Where once the light of its existence shone brighter than a star only a candle flickered.
Where it expected oceans of power it found only a few evaporating drops.
Where once fields of wisdom and knowledge sprawled to infinity only a few crumbling islands drifted in a sea of nothingness.
Where once its might spread across universes and dimensions, creating myriads of avatars to do the entity's every bidding, it was now confined to only a single spot besides the avatar of thought.
In fact, when the avatar observed from its outside vantage point the source was confined to a single lowly being, a human…. that couldn't be right. Even in its current extremely diminished state, the entity was far too powerful and complex to fit into such a pitiful form. With renewed vigor it scrutinized simultaneously its own structure, its current mortal shell and the universe it found itself in.
If it had been able to, the avatar would be shaking in horror. The entity had been caught in a nearly perfect trap, a magnificent, almost foolproof and immensely cruel multi-layered scheme. Its own power was twisted upon itself, steadily destroying its own substance, like a snake devouring its own tail and becoming less and less in the process. The trap itself was empowered by the energy release of this destruction, keeping the entity's soul contained to prevent the formation of an avatar developed highly enough to recognize the situation. The last part had obviously temporarily failed because of unknown reasons, albeit only long enough to allow the creation of the single avatar of thought. Formation of additional avatars or drawing more power from the nexus was once more impossible. Even now the avatar could feel the pressure to go back to sleep, to return to the mindform of a human, completely oblivious to the true nature of the universe and its own being. That was the next layer of the trap, forced reincarnation as a human or creature of similar properties. Judging from the amount of fragmentary memories that floated around in the nexus as fine dust the reincarnation process had already been repeated for untold eons.
The universe in which the flesh bag it was anchored to lived was one of these horrid things that ran exclusively on the cold hard laws of basic physics. No deities, no magic, no hyper- or subspace, no anything that could help it in one form or another. Sure, the avatar was able to bend or outright break the laws of that universe to some degree, but it would cost an extraordinary amount of power even for the smallest changes. It didn't help that most of the intact memories it had access to only dealt with magic in one form or another.
The who and why of its capture had been lost, among the overwhelming majority of other memories. The entity had even lost the knowledge of its own name and history. Most of what remained was completely unintelligible, either because of partial data loss or because the avatar wasn't developed highly or specialized enough to understand. The only thing clear was that the entity had been involved in a power struggle of the highest order, far beyond the meager grasp that it currently retained. Obviously the entity had lost. Badly.
The avatar didn't have the abilities to break the trap, and its power level was already sharply declining. Even if it somehow managed to dispel the trap, the entity's very being was damaged beyond repair. Its entire remaining soul structure was highly unstable and would rapidly collapse without the confining power of the trap. That left few options.
It could do nothing and again be completely imprisoned, its soul eroding further, which in turn would be reincarnated almost indefinitely until it was ground to nothingness and the trap dispersed due to lack of power. Each incarnation would be dimly aware of an immense loss, unable to ever find peace. Completely unacceptable.
The next option was to use its remaining free power to find another being of sufficient power and willingness to break the trap and in particular stabilize its soul, but that came with its own set of problems. Such a favor usually carried a heavy cost, and the entity had nothing of real value to repay it with. The best case would be its remaining knowledge in exchange for quick and painless destruction; the worst case would mean eternal thralldom to or absorption by its 'benefactor'. Beings of the necessary power level didn't deal in kindness. That was better than the first option, but not by much.
The last option would mean seeking out a being that was equally in dire straits and forge a very special pact, chaining them together forever. The entity would lose a large part of its remaining power, but it would be able to stabilize itself and begin anew the long climb to greatness, but this time with a partner to share its fate. Highly risky, but it seemed the best shot at surviving and retaining at least some power and free will.
Its decision made, the avatar cast its awareness outwards, rapidly seeking, analyzing and discarding the universes within its ever decreasing reach. In passing it noted that a nearby universe had recently been destroyed, resulting in an inter-universal shockwave which must have been what temporarily disrupted the trap. The entity needed someone desperate, for only the desperate would be willing to pay the price of the bargain it hoped to conclude. The avatar's hope dwindled as its search came up empty again and again. Each time where a world seemed promising some random factor made it unsuitable for the entity's needs. Finally, it found a promising candidate. The creature was in a unique position in its world's weave of destiny and possible futures that made it the ideal target for the entity's desperate gamble.
The world it belonged was a strange one, with magic existing even if the world's inhabitants were oblivious to its existence. Instead they used a peculiar energy composed of the powers of mind and body. The entity had no memory of ever encountering such a thing, but that didn't prove much. Even at the height of its power it had only possessed knowledge of a miniscule section of the infinite multiverse, and it was far from that happy state of affairs. This 'chakra' was unfamiliar, but could prove useful especially in its strangeness. There existed a limited number of higher beings in that world, but most were bound or otherwise indisposed and should therefore present no serious hindrances until the entity was settled and ready for them. Unfortunately the avatar had to cut the examination short because of its dwindling power level. It would need all its remaining power to transfer to that world, move to the target's location while maintaining control over the mortal shell of its prison and convince the target to accept the bargain. It had barely enough time to determine the optimal timeframe for presenting its proposal to the target.
There was no margin of error and no time to lose. Taking a metaphorical last breath, the avatar set its plan in motion. The entity stretched across the abyss between its current location and its target world, dragging its trapped core with it.
On an unremarkable planet in an unimportant galaxy in a universe like countless others, a completely average man vanished without a trace while sleeping in his flat. The following search initiated by his friends and family turned up nothing. In the end, he was just another unresolved missing person case.
In a distant world a small blond boy shivered in his sleep under his thin blanket, not knowing that another player had taken an interest in his destiny.