The History of Ninja off the top of my head:

Before the Time of Warring States in Japan there were many ethnicities which had a variety of feudal structures and loyalties.

By the end of the Warring States era Yoshimitsu Ashikaga was able to institute the bakufu system of government throughout Honshu.

Bakufu (as a noun for individual and plural beurocrats) became increasingly indifferent to the complex politics of post-genocidal Honshu.

"Hinnen," although I am not sure of that term, were then employed as messengers, spies, and eventually even did some of the muscle work (eg. killing unwanted elements at the lower levels of he Feudal system). In times of wider conflict they were also pressed into service to choose sides.

I dont recall exactly when, but a large Tantric Buddhist group was rounded up and systematically destroyed by one of the pre-Tokugawan Shogunates. The survivors of this group paradoxically (as Tantra is a peaceful love cult) created a militaristic separatist faction of these Untouchables who were employed to smooth the rough edges of the rigid and formalistic society of 15th/16th (I again am doing this all by rote) century Nihon.

They incorporated many of the folk styles of what would now be termed guerilla tactics from the provinces and included these styles (eg. costumes, weapons, ploys, etc.) with more modern Bushido techniques and systems of that era eventually forming what was termed in the Tokugawan era as Ninjitsu (in order that the government could identify, control, and even at times outlaw the system).

Think back to the hundreds of years of fighting in Japan, and imagine that in order to survive even farmers and fishers had to have small deadly devices which were undetectable to the roaming armies and hordes. This is the orgin of many of the more novel Ninja items and techniques.

Those of us who have studied Chinese Kung fu know that many of the weapons are actually farm impliments or even just a stick of bamboo from the nearest grove-- which peasants relied upon to defend themselves with in times of crisis.

To the best of my understanding that is the orgin of "Ninja."