The war initiated the Sengoku jidai, "the Warring States Period". This period was a long, drawn-out struggle for domination by individual daimyo, resulting in a mass power-struggle between the various houses to dominate the whole of Japan. It was during this time, though, that there would emerge three individuals who would later be considered the three great daimyo of the Sengoku Period, and who would eventually unite Japan under one rule; they were Oda Nobunaga, Toyotomi Hideyoshi, and Tokugawa Ieyasu.
By July 1467 the fighting had become serious, and this was when the Ōnin War is said to have started. By September, Kyoto's northern parts were in ruins, and everyone who could flee from Kyoto did so.
Both Yamana Sōzen and Hosokawa Katsumoto died in 1473, and even then, the war continued on, neither side figuring out how to end the war. However, eventually the Yamana clan lost heart as the label of "rebel" was at last having some effect. Ōuchi Masahiro, one of the Yamana generals, eventually burnt down his section of Kyoto and left the area. It was by 1477, some ten years after the fighting had begun, that Kyoto was now nothing more than a place for mobs to loot and move in to take what was left. Neither the Yamana clan nor the Hosokawa clan had achieved its aims, other than to whittle down the numbers of the opposing clan.
During this whole ordeal, the shogun was not instrumental in alleviating the situation. While Kyoto was burning, Ashikaga Yoshimasa spent his time in poetry readings and other cultural activities, and in planning the Ginkaku-ji, a Silver Pavilion to rival the Kinkaku-ji, the Golden Pavilion, that his grandfather, Ashikaga Yoshimitsu, had built.
The Ōnin War, and the shogun’s complacent attitude towards the war, "sanctioned" private wars and skirmishes between the other daimyo. No part of Japan was untouched by violence. Although the battles in Kyoto had been abandoned, the war had spread to the rest of Japan. In Yamashiro Province, the Hatakeyama clan had split into two parts that fought each other to a standstill. This stalemate, as well, was to have serious consequences. In 1485, the peasantry and ji-samurai (lesser samurai) had had enough, and revolted. Setting up their own army (the 'Ikki'), they forced the clan armies to leave the province. The Ikki were becoming a powerful force, much more than simply an armed mob. By 1486 they had even set up a provisional government for Yamashiro province.
The ikki would form and appear throughout the other parts of Japan, such as Kaga Province, where a sect of the Jodo Shinshu Buddhists, the Ikkō, started their own revolt during the Ōnin War after being enlisted by one of Kaga's most prominent warlords, Togashi Masachika. The Ikkō, who had a complex relationship with the Jodo Shinshu leader Rennyo, appealed to the common peasants in their region, and inevitably formed the Ikkō-ikki. By 1488 the Ikkō-ikki of Kaga Province expelled Masachika and the other warlords, and took control of the province. After this they began building a fortified castle-cathedral along the Yodo River and used it as their headquarters. The Ikkō-ikki and the Yamashiro-ikki were revolutionary, in a process called gekokujō ("the low oppress the high").
The Hosokawa family would control the shogunate until 1558 when they were betrayed by a vassal family, the Miyoshi. The powerful Ōuchi were also destroyed by a vassal, Mōri Motonari, in 1551; by the end of the Warring States Period only a dozen or so warlord families still remained standing. But the most important development to come out of the Ōnin War was the ceaseless civil war that ignited outside the capital city. Hosokawa tried to foment civil strife in the Ōuchi domains, for instance, and this civil strife would eventually force Ōuchi to submit and leave. From the close of the Ōnin War, this type of civil strife, either vassals striving to conquer their daimyo or succession disputes drawing in outside daimyo, was endemic all throughout Japan.
Scholars disagree on the appropriateness of the term "Warring States Period" (which is the Chinese term borrowed by the Japanese in calling this period "sengoku jidai"). Many argue that since Japan was essentially intact, the Emperor and shogunate remaining at least nominally in command of the whole country, it really wasn't a "warring states" period at all, but a "warring warlords" period. However, others such as Mark Ravina, Mary Elizabeth Berry, and Conrad Totman argue that the kuni (provinces) were not unlike quasi-independent states, and that the term is thus more or less appropriate.
The cost for the individual daimyo was tremendous, and a century of conflict would so weaken the bulk of Japanese warlords, that the three great figures of Japanese unification, beginning with Oda Nobunaga, would find it easier to militarily assert a single, unified military government.
Though it is classified as a work of historical military fiction (軍記物語), because of the time in which it was written, it is entirely possible that the author is relating a first person account of the conflagration. Though its author is unknown, his beliefs and philosophies are apparent throughout the text, as he relates the apparent futility of the war and the destruction it wrought on the capital. It remains an important work in part due to its departure from somewhat cut-and-dry depictions of the numerous battles, instead adding accounts of how the Onin War affected the city and its citizens:
"The capital which we believed would flourish for ten thousand years has now become a lair for the wolves. Even the North Field of Toji has fallen to ash ... Lamenting the plight of the many fallen acolytes, Ii-o Hikorokusaemon-No-Jou read a passage:
'Now the city that you know
Has become an empty field,
From which the skylark rises
And your tears fall.'