Uprising of the Iga Ninja Background to the conflict . During the Sengoku jidai Iga province was , due to a number of factors , not under the power of a daimyo ( feudal lord ) . Iga had achieved full independence and was controlled by a coalition of local goshi called Iga Sokoku Ikki ( 伊賀惣国一揆 , the " Iga republic " ) . This independence was achieved notwithstanding the fact that the strategic road Tokaido passed through Iga province . From the mid 16th century , Nobunaga by bloody wars began to unite Japan under his rule . Oda Nobunaga ' s son , Kitabatake Nobuto , after capturing the important province of Ise came to the border of Iga . A castle was built by his orders so that it could be used as a base for a future invasion of Iga , but the men from Iga recognize the threat and burnt it down right under his nose . Furious Kitabatake Nobuo took his samurais , without his father permission , and in 1579 marched into the Iga republic . Not expecting any real opposition , as they outnumbered the forces of Iga , and not prepared for their guerrilla tactics he was very humiliatingly defeated by a very underwhelming force . On top of this one of Oda Nobunaga ' s highly esteemed generals died during this catastrophic campaign . Of course this humiliation of the Oda family could not be allowed to stand , but at the time ( 1579 – 80 ) Oda ' s main forces were preoccupied . Due to this disgraceful event however , and as soon as he had the opportunity , Oda Nobunaga himself launched a new attack against Iga in 1581 from six different directions having mustered a force of 40 to 60 thousand men . This was about a ten times more manpower than the Iga forces could field , and during the campaign he slaughtered many of the Iga families . The Iga forces held - on to only two castles by the end when Oda Nobunaga declared a ceasefire and allowed some of them to escape ; many ended up taking refuge in the Kii province in the south . But one should not view this campaign only as an act of revenge , rather one has to see it in the light of the bigger political picture at the time . During this time several provinces opposed the ruling of the traditional samurai families and created , or tried to create , independent republics governed by a coalition of jizamurai s , peasants , wealthy merchants and various religious sects . One of the most famous and the most powerful was the religious Ikkō - ikki movement that took control over several provinces from 1496 to the mid 16th century . In 1560 Matsudaira Motoyasu ( later known as Tokugawa Ieyasu ) as well as his later rival Toyotomi Hideyoshi were both allies of Oda Nobunaga . Matsudaira Motoyasu was the first of them to fight with the Ikkō - ikki movement at the Battle of Azukizaka in 1564 in his attempt to pacify the movement in his home province Mikawa . In 1570 Oda Nobunaga started the siege of the Ikkō - ikki s primary fortress Ishiyama Hongan - ji in modern day Osaka . It was believed to be impenetrable and could summon more them ten thousand warrior monks with a ring of a bell . This siege boxed in the Ikkō - ikki ' s forces as well as blocking supplies . At the same time he attacked and laid siege on several other Ikkō - ikki controlled positions their among Nagashima fortress complex in Owari province along Japan ' s Pacific coast . He attacked Nagashima three times ; 1571 , 1573 and 1574 before he finally to destroyed the fortress complex and all it ' s forces . After that he could in 1576 focus his forces to the siege of the Ikkō - ikki s primary fortress Ishiyama Hongan - ji . In 1580 Ishiyama Hongan - ji surrendered after having managed to endured the longest siege in Japanese history . The entire temple complex went up in flames and with the destruction of the Ishiyama Hongan - ji the might of the Ikkō - ikki was broken and the slaughter of its followers and allies could begin . South east of the Ishiyama Hongan - ji in the Kii province another ikki was in control . This movement was known as the Saika Ikki lead by Saika Magoichi , based in Ōta castle och backed by the warrior monks , Negoro - gumi , of the Negoro - ji - famous for their skills with arquebus as well as for their expert gunsmiths and foundries . It is possible that the Saika Ikki was not directly part of the Ikkō - ikki in the Ishiyama Hongan - ji but certainty they were their ally as they helped the them during the Siege of Ishiyama Hongan - ji with both manpower and supplies . As a result Oda Nobunaga lay siege on the Ōta castle in 1577 - however this seems to have been more of a box in maneuver to prevent their intervention then a siege with the aim to actual destroy the castle . The Saika Ikki is very important in the context of Iga no ran because they was in control over the territory to where many of the refuges from Iga ended up after the destruction of Iga Sokoku Ikki in 1580 . These territories would later be transformed into the Kishu domain ( also known as Kii domain or Wakabe domain ) , and is the birthplace of the Ninjutsu school called Kishu ryu which later change it ' s name in to Natori ryu that is belived to have its roots among the schools from Iga . Later , after the death of Oda Nobunaga during the Honnō - ji Incident in 1582 , the Negoro - gumi of the Negoro - ji would become allies of Tokugawa Ieyasu against Toyotomi Hideyoshi in the Battle of Komaki and Nagakute in 1584 and as a response to this Toyotomi Hideyoshi lay Siege of Negoro - ji in 1585 and burnt the Negoro - ji temple complex down . The same year Toyotomi Hideyoshi forces lay Siege of Ōta Castle to where many refugees from Negoro - ji had fled and destroyed it and thereby even the Saika Ikki - refugees from the two battles is said to have joined Tokugawa Ieyasu forces . All this is roughly happening at the same period of time as Hattori Hanzo helps Tokugawa Ieyasu flee back to his home province after Oda Nobunaga death at the Honnō - ji Incident through the network of Iga families and a large group of the men from Iga pledge allegiance to Tokugawa Ieyasu in 1582 . Interesting is that Suzuki Shigehide , the son of the leader of the Saika Ikki ( both known under the name Saika Magoichi ) , is said to have lived the rest of his life as a rōnin in Mito Domain after the death of Torii Mototada , who served Tokugawa Ieyasu and is said to have had help of big troupe of ninja s , in the beginning of the battle of Sekigahara in 1600 . This could incline that the whole Saika - Ikki , and not only the monks at Negoro - ji , became Tokugawa Ieyasu ' s allies roughly at the same time as the ninja clans from Iga and that Suzuki Shigehide after the destruction of Ōta castle and the Saika Ikki swore his allegiance to Torii Mototada . In 1619 the territories formerly controlled by the Saika Ikki officially was transformed into the Kishu domain , founded by Tokugawa Yorinobu and thereby placed directly under the rule of one the three Gosanke ( " Three Houses of the Tokugawa " ) called the Kii Tokugawa or Kishu Tokugawa . When Tokugawa Yoshimune ( ruled 1716 - 1745 ) later dismissed all the Iga ninja from his intelligence network he replace them with men from just the Kii province . The big threat from the various ikki was more due to the economic and political threat they posed then their actual military might . The Ishiyama Hongan - ji and other strongholds of the different ikki lay across major trade routes and occupied the same areas that Oda Nobunaga saw as his primary territories . Nearly every road to the capital was controlled by the ikki or their allies , and the populist roots of the ikki movement gave them significant economic power as well . Oda Nobunaga in particular sought the destruction of the Ikkō - ikki for these reasons , and because they allied themselves with nearly every one of his major enemies or rivals . The Iga Sokoku Ikki was part of this pattern and not only an independent and powerful mercenary force as well as a political wild card but also was very close to the very important Tōkaidō road and as such they was a potential threat to the supply lines between east and west . Due to this it was only logical from a military strategic point of view to somehow subdue this independent force . And after the humiliating defeat of his son he had no other real choice than to destroy them .