Long ago, magic and science existed side by side. Eventually science overshadowed magic, and it faded into the shadows, never heard from again.
This science destroyed the world, nuclear missiles ravaged the planet. Decades passed, 90% of the world's population killed. The rest, they adapted. Evolved. One man amongst them grew to the greatest lengths of known history. They called him a Sage, a man capable of using mystical energies to do his bidding. He gave the gift of magic to the people, inspiring them with hope, and abolishing despair.
However, another man stood in his way. This man sacrificed himself to the Old Gods, and summoned a Hell General known only as Ippon-datara, the Ame no Hitotsu no Kami, Deidarabocchi. This beast was unstoppable, so the Sage did the only thing he could.
"Sealing, NOW!"
With the cry of his magic, the Sage sealed the beast inside him, at the cost of causing him to slowly die. The Sage, on his death bed, gave his legacy to his two sons, Ryuu and Tatsu. These two would later sire the Senju and Uchiha clans respectively. Ryuu was blessed with the indestructible magical body of his father, while Tatsu gained the eyes of the Sage. While he gained the more powerful eyes, which were mutated from the Hell General's magic energy, Tatsu grew jealous, and eventually his hatred passed onto his clan's. The Senju and Uchiha would always be enemies.
Years in the future, present day
In this time and age, the true magic has been lost, replaced by the bastardized version known as chakra. The Sage's teaching forgotten by all but a few. However we have broken through, one boy, a new graduate in the Ninja Academy of Konoha, is about to turn his tears into jewels.
Now, it's showtime!