The Rise and Fall of the Ninja:
The fearsome Ninja really came into their own during the turbulent era between 1336 and 1600. This was a period in time in Japan that was fraught with constant war, and Ninja skills were in hot demand by all warring factions.
During the Sengoku Period, from 1467-1568, Ninjas acted as spies, assassins, agitators, scouts, and surprise attackers. They were extremely effective in besieging a castle, as they could infiltrate and distract the defenders on the inside while the main army attacked from the outside.Destruction of the Ninja Bases (1581)
Although the Ninja were a valued and often used tool during the Sengoku Period, they were also a destabilizing influence. When the warlord Oda Nobunaga came out of all the fighting as the strongest daimyo, and began reuniting Japan during 1551-1582, he saw the Ninjas as a threat and a force to be reckoned with.
Nobunaga staged a lightning quick attack on Iga, one of the main Ninja strongholds, and forced them to fight openly. Open battle not being the Ninja strong suit, they were defeated, and disbursed to nearby provinces or the mountains.
Even though their stronghold and power base was destroyed, the Ninja did not completely vanish. Some Ninjas went into the service of Tokugawa Ieyasu, who went on to become Shogun in 1603.
The Ninja, reduced in numbers, continued to serve both sides in disputes and struggles. In a noted famous incident from 1600, an intrepid Ninja infiltrated the gates of the enemy, and sneaked through a group of Tokugawa's defenders at Hataya castle, where he proceeded to plant the flag of the besieging enemy army on the front gate.
Edo and the End:
The Edo Period in Japan, from 1603 through 1868, brought sorely needed peace and stability to Japan. It also brought the story of the Ninja to an end. This ending was portrayed in the movie "The Last Samurai" with Tom Cruise. But, Ninja skills and legends survive to this day.