The Era of the Warring States (戦国時代, Sengoku Jidai) was an extremely lengthy and bloody period in history where hundreds of individual shinobi clans fought in constant, bitter warfare. It ended when the Uchiha clan and the Senju clan formed Konohagakure.
Following the death of the Sage of the Six Paths, the various shinobi clans began to form governments among themselves, with his two sons going their separate ways. Peace only lasted five years following his death, however, before the lesser clans, which were dominated by the stronger, more independent shinobi clans, rose up to overthrow their overlords in a period known as "gekokujō" (下克上, "the underling conquers the overlord"). During this time, the Uchiha Clan formed under the reigns of the Sage's grandson, Ryun Uchiha, while the Senju Clan formed under the reigns of Mataiden Senju. Lesser clans, such as the Hyūga Clan and the Kurosaki Clan, formed under the leaderships of Seireitou Hyūga and Hikaru Kurosaki respectively. The lands began to carve out their territories, and several daimyō began to claim leadership of these lands, filling the vacuum left by the shinobi warlords.
Sometime after that period, the Ōnin War (応仁の乱, Ōnin no Ran), which set off this period of ninja wars, began as a civil war between the Hyūga and the Kurosaki clans — both clans wanting their leader to become the "shogun" of a large territory in the modern day Land of Earth. The leaders of these clans, Seireitou and Hikaru, despised one another a great deal, and their bloodshed soon drew other clans in. This was the first official war that the Uchiha joined in on, using their Sharingan to dominate the battlefields. Eventually, the Uchiha sided with the Hyūga, their clan leaders becoming friends following a battle that took place deep in what would become the Land of Fire. It was after this, during the ensuing conflicts, that Seireitou became the first Hyūga to awaken the Byakugan. In a bid to end the war, Ryun, the leader of the Uchiha, enslaved a young Kurama, the Nine-Tails, with his Sharingan, using its superior power to obliterate the Kurosaki ninja.
This, in turn, lead the Kurosaki to capture and control Shukaku, the One-Tail, in the hopes that it would even the playing field. This would later lead to a hate-filled blood feud between the two tailed beasts. Ultimately, however, the war was fought to a bitter stalemate, though the Kurosaki Clan later lost its drive, and retreated, causing most to believe the Uchiha and the Hyūga truly won the war. Nevertheless, this war acted as a catalyst for others, as the clan warfare had ruffled the feathers of other clans that had been influenced by the war, causing a period of constant, unending civil war, which would last nearly a century before it was finally, peacefully, brought to a close.
As the ninja wars raged on, the samurai (侍), who had been the ruling military power prior to the Sage of the Six Paths, began to see the shinobi as a threat, and began to war with the various shinobi clans. However, at this time, samurai had not yet learned to use chakra, and the shinobi quickly began to push them back. These conflicts only lasted two years, according to Ryun Uchiha, as the last remaining pockets of samurai were pushed into the Land of Iron.
Uchiha—Senju Blood Feud
After the fall of the samurai, the new daimyō began to hire shinobi clans to fight against one another as they fought for control of the new countries. During this period, two of these clans came to the forefront; the Uchiha clan and the Senju clan. The clans became so prominent that, should one leader hire the Senju, the other would hire the Uchiha. The leaders of the clans, Ryun and Mataiden, had been close friends prior to the war, but, due to the necessity of their occupation, became rivals. Ironically, however, they still saw each other as best friends, never intentionally trying to kill the other. This began to arouse anger in both clans, as the death of either clan's members tolled heavy on their people. Eventually, the Uchiha decided to finish Mataiden off for themselves, assassinating him at his clan's headquarters. This event pained Ryun so much, that his Mangekyō Sharingan awakened, and he became a far more brutal leader. After discovering the Uchiha's involvement in his friend's death, however, he entrusted the clan to his sons, Madara and Izuna Uchiha, and left.
Due to the unrelenting violence, the average life-span for a shinobi was a mere 30 years during this time, though the single biggest reason for the continuing fall in life expectancy was the slaughter of countless conscripted children. With the continued loss of their kin, a never ending cycle of death and revenge was born, which saw shinobi having to even conceal their surnames for fear of retaliation. Hashirama Senju, Mataiden's oldest son, and Madara's former best friend, took the reigns of the Senju clan following his father's death, and continued the war with the Uchiha. Madara, who blamed the Senju for his father's departure, turned away from Hashirama's friendship, and thus, a bitter rivalry developed between the two young men. During this time, Madara and his brother discovered the secret of the Sharingan; becoming the first, next to their father, to awaken the Mangekyō Sharingan. Though with the constant battles, Madara's vision degraded further and further until he decided to take his brother's eyes, gaining an "Eternal" Mangekyō Sharingan with which to keep fighting.
After decades of conflict, most of the clans under the Uchiha and Senju banners formed the first lasting truce after growing weary of the continued bloodshed. The only person who opposed this peace was Madara, who argued for the Uchiha clan to continue the fighting, but was ultimately persuaded to join in a permanent alliance with the Senju clan. Soon after, a pact was formed with the Land of Fire and thus, Konohagakure was formed. This set a precedence which others soon followed, creating the Five Great Shinobi Countries, as well as some smaller, outlying villages and settlements.
The Sengoku Period (戦国時代, Sengoku Jidai), or Warring States Period, was a time when Japan was in civil war and the demand for ninja was high. This moment in history was the time of many of famous ninja, including Hattori Hanzō. But after the war resolved, their services were cut in a united Japan and, ninja began to fade into history.