Shinobi History
In the later 14th Century Ce, Japan was fractured and falling apart socially. Shoguns and daimyos, warring for dominance, all had their personal assassins, trained in esoteric but mortal methods of discreet warfare. This fragmentation has also broken the power of the Shinto pantheon, as worshippers start to drift more and more apart and the gods bicker over increasingly weaker domains.
The Dutch arrived in 1640 and the introduction of trade and other religious beliefs starts to weaken the Shinto pantheon even more.
The Shinto pantheon joined together to start the first school for training Shinobi, with priests acting as sensei and spiritual leaders alike. It's super idiosyncratic because every god has their own school of magic, combat, and tactics. But they more or less cooperated with all schools under one roof for the first time. Students of the Shinobi College start developing magical talents as well as refining esoteric physical ninja skills. As they mastered increasingly difficult and arcane methods and secret instructions, their magical talents continued to advance. The champion of each individual school became the Emissary for their god, a true Shinobi and empowered with unique and divine power from their patron.
From those schools, the most worthy Shinobi was selected to represent the entire pantheon's interests. It's a lifetime appointment-- keyword 'lifetime'. These ascendants are 'True Shinobi', literally divine emissaries of the Shinto pantheon and formidable peers to demigods themselves.
The first schoowl was founded in Koga. A second one was opened up in Igo not long after, as several of the female deities broke away to form a college for training the women (the Kunoichi). Much tension exists between the gods of the schools, though their followers tend to find more reasons to cooperate than distruest one another.
Around 1730, an ambitious young Shinobi candidate was passed over for appointment to the Divine Shinobi title. Humiliated and angry, he stole much forbidden knowledge, murdered the Sensei, and forsakes forsook his oaths of silence. He found the darkest shadows in Japan and mades profane sacrifices to whomever would heed him. His prayers were answered by an ancient and malevolent entity call The Beast. In exchange for giving the Beast all the secret knowledge of the Shinobi, he was empowered by The Beast with dark and terrible magics. He became the Dark Shinobi, and started a secret guild of magically-trained assassins which was eventually called The Hand. Assassins, poisoners, provocateurs and sabotagers, they would sell their talents to anyone with the coin-- or donate their assistance to anyone who advacned their causes.
Over time, shoguns and daimyos copied the Shinobi method and start their own schools and secret monasteries. Some of these schools unlocked their own magical esoteries, though few of them came close to the power of a true Shinobi. Still, these agents of espionage became what people in the larger world consider 'Ninja' in modern parlance.