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well,
as most of you probably know, they were all a fearsome force during the 1500's... And they had various complexes and allegiances throughout the time.
The only question is...
Which ones were located where. And to what religious sect(s) did they belong?
I have some personal knowledge, but let's see what everyone thinks/would like to know. (looks in Seal's direction)
-Zen Blade
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Zen Blade Asai
Red Devil
Last of the RSG
The most famous of the religious groups was the Honganji, adherants of the Jodo-Shinshu. At first located in Kyoto, their headquarters was later rebuilt roughly where modern Osaka is. The Ishiyama Honganji (the previous temple was called the Yamashina Honganji) became a great stronghold, and resisted Nobunaga for many years. Even when that place surrendered in 1580, the Honganji remained on the scene. In 1591 Hideyoshi invited the Honganji to built a new temple - albiet and of course of a non-militant nature.
By 1531, the Honganji had become the effective rulers of Kaga Province through a complex series of events that saw the former shugo of that place, the Togashi, eclipsed. While the Togashi are often described as being forced out by the people of Kaga, they actually remained as shugo (however nominally) there until the early 16th Century. Prior to the civil war in 1531 that consolidated Honganji rule, the situation in Kaga was confused. In 1531, Togashi Taneyasu was expelled and the various ikki factions more or less brought into line. The Honganji established a governing body at present-day Kanazawa and made Kaga into a formidable domain. Ikki were also strong in neighboring Echizen and Etchu (where they defeated and killed Uesugi Kenshin's father in the 1530's). The Echizen ikki resisted Nobunaga's occupation of that province (Oda had taken it from Asakura in 1573) and in 1574 rose up, killing Asakura Kageakira. Their primary army was defeated in 1575, though it would not be until around 1580 that the Oda could claim that Kaga was subdued.
Elsewhere, strongpoints of Jodo-Shinshu resistance could be found in Ise (at Nagashima) and Owari (finally brought down by Nobunaga in 1574 and 1575)) and Mikawa (subdued by Tokugawa Ieyasu during the mid-1560's). In Kii Province, militant Negoro and Jodo-Shinshu adherants supported the Ishiyama Honganji and where themselves forced to submit when Hideyoshi moved against them in April 1585. The fall of Saiga (coming soon after the Negoro) marked the end of the last real Shinshu resistance.