The battle of Sekigahara is Japan's most notorious, and it was certainly one of the largest (if not the largest) in its recorded history. It was the culmination of the civil war between Tokugawa Ieyasu, daimyo of the Kanto plain and his rival Ishida Mitsunari.
The preliminary moves of the battle of Sekigahara consisted of a spate of attacks and sieges on castles, including the castle of Fushimi to the south-east of Kyoto. Toyotomi Hideyoshi had unified Japan and consolidated his power following the Siege of Odawara in 1590, his ill-fated invasion of Korea significantly weakened the Toyotomi clan's power as well as the loyalists and bureaucrats that continued to serve and support the Toyotomi clan after Hideyoshi's death.
Hideyoshi's and his brother Hidenaga's presence kept the two sides from anything more than quarreling, but when both of them died, the conflicts were exacerbated and developed into open hostilities. Since the Toyotomi clan was known to be descended from peasant stock, neither Hideyoshi nor his heir Hideyori would be recognized or accepted as Shogun.
Later, a supposed conspiracy to assassinate Ieyasu surfaced, and many Toyotomi loyalists were accused of taking part and forced to submit to Ieyasu's authority. However, Uesugi Kagekatsu, one of Hideyoshi's appointed regents, defied Ieyasu by building up his military. When Ieyasu officially condemned him and demanded that he come to Kyoto to explain himself before the emperor, Kagekatsu's chief advisor responded with a counter-condemnation that mocked Ieyasu's abuses and violations of Hideyoshi's rules, in such a way that Ieyasu was infuriated.
Afterwards, Ieyasu summoned the help of various supporters and led them northward to attack the Uesugi clan, which at that moment were besieging Hasedō, but Ishida Mitsunari, grasping the opportunity, rose up in response and created an alliance to challenge Ieyasu's supporters, also seizing various daimyo as hostages in Osaka Castle.
Mitsunari then officially declared war on Ieyasu and lay siege to the Fushimi Castle, garrisoned by Tokugawa retainer Torii Mototada on July 19. Torii’s forces had to defend themselves against the armies in the west long enough for the Tokugawa army to regroup for the fight in Seki Ga Hara in the east.
There were 400 ninjas from Koga Ryu who were called into action and aided with the defense of Fushimi Castle. Some of the ninja were in the castle, while the others terrorized and harrased the enemy outside with different kinds of raids. About 100 of the Koga ninja were killed in the battle.
Afterwards, the western forces captured various Tokugawa outposts in the Kansai region and within a month, the western forces had moved into the Mino Province, where Sekigahara was located.
Back in Edo, Ieyasu received news of the situation in Kansai and decided to deploy his forces. He had some former Toyotomi daimyo engage with the western forces while he split his troops and marched west on the Tōkaidō towards Osaka Castle.
Ieyasu's son Hidetada led another group through Nakasendō. However, Hidetada's forces were bogged down as he attempted to besiege Sanada Masayuki's Ueda Castle. Even though the Tokugawa forces numbered some 38,000, an overwhelming advantage over the Sanada's mere 2,000, they were still unable to capture the strategist's well-defended position. At the same time, 15,000 Toyotomi troops were being held up by 500 troops under Hosokawa Fujitaka at Tanabe Castle in Wakayama Prefecture. Some among the 15,000 troops respected Hosokawa so much they intentionally slowed their pace down. Both these incidents resulted in a large number of Tokugawa and Toyotomi troops not to show up in time at the battlefield of Sekigahara.
Knowing that Ieyasu was heading toward Osaka, Mitsunari decided to abandon his positions and marched to Sekigahara. On September 15, 1600 the two sides started to deploy their forces. Ieyasu's eastern army had 88,888 men, whilst Mitsunari's western army numbered 81,890. There were about 20,000 arquebusers and other forms of hand-held gunners deployed in the battlefield, corresponding to over 10% of all troops present.
Even though the western forces had tremendous tactical advantages, Ieyasu had already contacted many daimyo on the western side, promising them land and leniency after the battle should they switch sides. This led some western commanders holding key positions to hesitate when pressed to send in reinforcements or join the battle that was already in progress.
Mori Hidemoto and Kobayakawa Hideaki were two such daimyo. They were in such positions that if they decided to close in on the eastern forces, they would in fact have Ieyasu surrounded on three sides. Hidemoto, shaken by Ieyasu's promises, also persuaded Kikkawa Hiroie not to take part in the battle.
Even though Kobayakawa had responded to Ieyasu's call, he remained hesitant and neutral. As the battle grew more intense, Ieyasu finally ordered arquebusiers to fire at Kobayakawa's position on Mount Matsuo in order to force Kobayakawa to make his choice. At that point Kobayakawa joined the battle on the eastern side. His forces assaulted Yoshitsugu's position, which quickly fell apart as he was already engaging Todo Takatora's forces. Seeing this as an act of treachery, western generals such as Wakisaka Yasuharu, Ogawa Suketada, Akaza Naoyasu, and Kutsuki Mototsuna immediately switched sides, turning the tide of battle.
The western forces disintegrated afterwards, and the commanders scattered and fled. Some, like Ukita Hideie managed to escape, while others, like Sakon was shot and wounded by a rifle though it's unknown if he died from it, Ōtani Yoshitsugu committed suicide. Mitsunari, Yukinaga and Ekei were some of those who were captured and a few were able to return to their home provinces. Mitsunari himself would be executed.
Ieyasu already had great repect for the Koga ninja since thier attack on Kaminojo in 1562. However the service of the koga ninja at Fushimi far surpassed that of the attack on Kaminojo. About 100 of the Koga ninja had been killed in the battle at Fushimi Castle, and after the successful conclusion of the Sekigahara campaign, Ieyasu held a memorial service commemorating the dead.
According to tradition, the legendary Miyamoto Musashi was present at the battle among the ranks of Ukita Hideie's army. Supposedly, he fought well and escaped the defeat of Hideie's forces unharmed. Whether this is fact or myth is unknown, considering that Musashi would have been around 17 years of age at the time. Several books on Japanese history, martial arts and the biography proceeding a translation of the'Go Rin no Sho' mention Musashi joining the ranks of the Ashikaga army and escaping the hunting down and massacre of the vanquished army. More curious is the fact that he joined Tokugawa in both winter and summer campaigns of 1614 and 1615 when Ieyasu laid siege to Osaka castle where supporters of the Ashikaga family gathered in insurrection, thereby fighting against those he had originally fought for at Sekigahara . According to legend, Musashi had already killed in self defense at 13 and again at 16 defeating Tadashima; he then left home on his 'Warrior pilgrimage' which saw him victorious in scores of contest and which took him to war before he was 17.