So this is based on the original history of shinobi that doesn't the Otsutsuki Clan and the God Tree. It isn't canon compliant but you could think of it as what is mistakenly believed to be the true history of the Narutoverse, masking what really happened all those years ago.
False Origin of Shinobi (
Official Version)
Chakra is an energy that has existed within the world and all living creatures since the very beginning. It flows through the veins of the earth and of humans and beasts alike.
But the people of this world knew little of chakra and had no way of wielding it. It was a power that existed within all but none could touch.
Then a thousand years ago, a special child was born with a connection to chakra unlike any other. It was as if he was a chakra point for the entire world and this manifested in the form of the Rinnegan, the first and most exalted of doujutsu.
The child, Hagoromo, could see and comprehend chakra on a fundamental level and thus wield it as an extension of himself. He bent the elements to his whim, confused the minds of men, enhanced the strength of his body, created form out of nothingness and breathed life into form. He was even blessed with the power of the Six Paths and the Outer Path and he delved into the mystery of chakra until the body, spirit and all of nature held no secrets for him.
Hagoromo did not believe he should hoard this knowledge for himself and instead shared it with the world. He lived in an era of endless war and believed that the gift of chakra would bring it to an end.
If people knew how they could shape the world, how they could connect their spirits to understand one another and how they could tap into their own potential to discover who they truly are, what need could there ever be for war? Hagoromo travelled across the entire land, quelling conflict with his great power and teaching the nature of chakra to all who were willing to learn, human or otherwise.
He named the arts that he had created Jutsu and classed them as Ninjutsu, Taijutsu and Genjutsu, breaking them down into their own categories and types and then even further into individual jutsu. He developed hand-seals to shape and transform chakra in those who lacked his impossible flair for chakra manipulation. Hagoromo's power, wisdom and desire for peace earned his title as the Sage of Six Paths and, in time, this great following became known as the Shinobi Sect.
But centuries of warfare and bloodshed committed by humanity had tainted the world with its malice. It seeped into the earth and flowed within the chakra of planet, growing until it gained a will and life of its own and held nothing but hatred for the race that birthed its foul existence. It rose up to bring an end to all things.
And so the Ten Tailed God was born, a monument to humanity's sins.
The Sage of Six Paths fought that god and the Shinobi Sect fought the beings that split from its body. It was a war unlike any other to protect themselves from extinction. In the end, Hagoromo sealed the god's body within a titanic prison of stone where it should remain trapped for all eternity in the void between worlds. And he sealed its chakra within himself to ensure it would never have the power to escape which transformed him into an entity greater than ever before.
He could move through the sky like a creature of flight, transform his body in strange new ways, control all forms of nature around him and mix together any and all of his nature transformations to create even more jutsu.
From that day Hagoromo became known as the God of Shinobi.
Hagoromo eventually had two twin sons, Indra and Asura, whom the Shinobi Sect had great expectations for. Indra was a genius who inherited the power of his father's eyes and Asura was a fool who inherited the strength of his father's body.
They were the closest of friends and the greatest of rivals who understood each other on the level that no one else could come close to. For all that, their life experiences gave them two entirely different ideas on how to create peace.
Indra's prowess led him on a solitary life where he needed to depend on no-one and believe that strength and force were the key to peace. He was born with the Sharingan which could copy jutsu, predict movement, hypnotise the mind and even granted him unique jutsu such as Susanoo.
Asura's ineptitude taught him the value of others as he befriended and was support by many others, teaching him that love was the key to peace. He had no inherent abilities aside from a tough body full of vitality but after years of dedication he awakened the Six Paths Senjutsu, drawing on the world itself to empower him.
Hagoromo could have lived forever if he desired but he felt it would be best to pass on his mantle to another generation instead of trying to rule the world himself. Hagoromo created nine tailed beasts from the Ten Tails’ chakra; he gave them names, taught them of the world and allowed them to be free to live how they chose until they could find their place in the world.
At the end of his life, Hagoromo chose Asura to lead the Shinobi Sect in his place as he chose to believe that love was the key to peace. He passed away but those left behind were left unsatisfied.
Indra felt betrayed by his choice and crossed blades with Asura in his desire to take his place as their father's rightful successor. The conflict between them was long and bitter, poisoning the Shinobi Sect as its followers chose to side with each of the brothers. In the end, Asura and Indra killed each other in battle and any hope of peace was destroyed.
The Shinobi Sect continued to follow their example as they became warring clans that only used chakra to kill each other, all of their jutsu devised for the sake of hurting and deceiving their enemies. And the brothers' feud was passed onto their children and their children's children in a conflict lasting so long that those involved have no idea how it started.
The strongest bloodline of the brothers would become the Senju, Uchiha, Uzumaki and Hyuuga clans. But many others clans and individuals possessed the blood of the Sage which often manifested in unique abilities passed down to each generation, all spawned from the power of the Ten Tailed God.
Soon enough, the Shinobi Sect became Shinobi and lost their ties to their beginnings. Even a thousand years later, the wars rage on and the Sage of Six Paths watches over the world in hope that someone would finally bring peace.
