The history of Ninjutsu is closely tied to that of Japan. One thousand years ago several family clans dwelt in the wooded mountainous regions of south central Japan. These families practised pragmatic ideals in the search for individual enlightenment using teaching that had originated in Buddhist Tibet and had travelled to Japan via T’ang dynasty China.
The powers controlling the state religion did not accept the theory that spiritual enlightenment could be experienced directly by anyone less than a priest of the ruler’s religion. Troops were deployed to eliminate these rural troublemakers. So, the families had to employ the knowledge gained through their studies of nature and the human body and mind in a martial direction as the necessity for protection against danger grew. The resulting centuries-long struggle for religious independence produced the legend of the supernatural ninjas.
As Japanese history unfolded, the ninja families evolved into military specialists. The increased demand for ninja agents required a training system that could produce espionage or combat specialists in the shortest possible time period. Physical tricks came to replace the developed natural abilities of the original mystics. Systems of combat skills based on the deception of the senses became the ninja’s stock-in-trade. These individuals, once motivated by love for their families, came to be feared for the ruthlessness of their determination.
From the 13th to the 17th centuries in Japan, countless ninja families operated out of a wide range of motivations and levels of sophistication. Each family or clan had its own specific requirements for status as a ninja agent. Some groups stressed physical skills, others mental alertness or political contacts.
During every active day of a ninja’s life, he or she was exposed to new and unfamiliar environments and experiences. Their learning system had to general enough and broad enough in scope to provide them with a means of handling any situation that came along. Much of the ninja’s practical knowledge of the world could be labelled as working common sense or “awareness”. Socially, far below the elite samurai status with its rigid codes of honour and propriety, the ninja were free to apply the naturalist teachings of their heritage and follow the path of ninpo for moral guidance.
The above information is paraphased from Stephen Hayes, "Spirit of the shadow warrior" 1980
Prior to the Mongol invasions, Japanese warfare involved duels between mounted samurai of equal rank supported by groups of retainers. The Mongols disregard of Japanese military etiquette and their successful use of large scale infantry spearmen forced an evolution of Japanese strategy to mimic that of the Mongols. This led the Daimyos to create larger infantry armies which resulted in the age of warring states. It is to be noted that the 2nd Mongol invasion was halted by poor sea conditions and changing political targets and not by Japanese military might.