The ninja cult originated and is based on the romance linked with the lives of spies and assassins in historical Japan. Legend says that in the 4th century a prince, Yamato Takeru disguised as a beautiful maiden assassinated two chieftains of the Kumaso tribe. In the 14th century there is reference to a highly skilled ninja or shinobi who was credited to have destroyed a castle by fire. From the 15th century onwards spies were officially trained and the word shinobi defined a secretive group of spies. The strategy was taken up by the Chinese military also.

In the 15th century ninjas were hired for purposes of raiding. They were terrorists and arsonists par excellence. In contrast the samurai of Japan fought open duels. But during troubled times of Sengoku period there was great demand for ninjas and less importance was given to respectability. The ninjas became spies, experts in ambush attacks and spreading agitations. There were families of ninjas who formed big guilds each having its own territory. Within them there was ranking with the jonin being the upper man, the chunin being the middle man and the assistants being jonin. The lowest was the lower man or genin. The latter were recruited from the lower ranks and sent out to the forefront of trouble.

Following the siege of Osaka in 1614 the ninjas again came to be employed. Miura Yoemon was a ninja employed by warlord Tokugawa. He hired more ninjas from the Iga clans and sent ten of them to Osaka Castle. It is worth to mention here that the ninja's who came from clans. In the pre-modern ancient Iga Province lived the Iga and Koga clans. In this region the villagers were mainly engaged in being trained to be ninjas. After one such decisive victory the Iga ninjas became guards for the inner territory of Edo Castle near modern Tokyo. The ninjas of the Koga clan got appointments in the police force and helped in guarding the exterior gates of the castle. In that time Japan was originally known as Ozakajo. Osaka played an important role in the unification of the country in the 16th century.

The ninjas took a pivotal role during the peasant rebellion known as Shimabara Rebellion in the 17th century. The peasants were largely Christians. The Koja ninjas were employed by a shogun - a person of military rank.

In the first years of the 18th century shogun Tokugawa Yoshimune set up an intelligence agency, Oniwabanshu, comprising of the ninjas. It secured information for reasons of national security. The group comprised of onmitsu ninjas who sniffed out all the activities of daimyos and government servants.

The daimyos was powerful warlords in medieval times who ruled over the major parts of the country from their huge inherited landed property. In the late 16th century Oda Nobunaga, aggressively conquered nearly a third of the other daimyos and after invading Iga province exterminated the organized ninja clans. The survivors fled and were scattered. In some places they were made most welcome for obvious reasons. Many took shelter in the Kii Mountains.

The ninja's who was specialized in unorthodox methods of warfare. With the help of ninjas the war lords in medieval Japan exterminated enemies and established their supremacy.