Foreword
Let me quote from "Introductory History - To the Schools of Bujinkan" by Paul Richardson (1995, 4th Ed, Bujinkan Lincoln Dojo):

"Japanese history is possibly the most recorded on the spot history by any nation in the world. Unfortunately, the winner always writes the history, in the way that he sees it. Because almost all Japanese history was written by the Samurai, very little mention of the Ninja exists. Even Hanzo Hattori, a prominent Ninja leader, is recorded as being Samurai. He may well have been a Samurai, as well as being a Ninja."

So, do not look upon the contents of this page as hard facts, but rather as rumors, opinions and fragments. And secondly, don't be fooled into believing that one can capture the 'feeling' of bujinkan from history. Feeling can only be optained during training. I'm certain that this page holds more value to an experienced practitioner of Bujinkan than to the casual reader. Read on and see if you agree!

After each section it will be stated from where I optained that particular information in a smaller font.

Togakure Ryu
School of the Hidden Door
The Togakure school of ninjutsu dates back to Togakure Daisuke in the period of Oho (1161-62). He recieved his training in ninjutsu from Kagakure Doshi. One July [day] during the Hogan period (1156-59), Shima Kosanta Minamoto no Kanesada, aged 16, and a powerful clan in the Ise province, joined the army of Minamoto Yoshinaka and fought with [against] three thousand horsemen horsemen of the Fujiwara Hidehira army. Lying fallen in the battlefield seriously injured, Shima was saved by Kagakure Doshi and they fled into the mountains of Iga. It is said that he recieved his training martial arts as well as ninjutsu from Kagakure Doshi. In later years he was celebrated as the second grandmaster of the Togakure ryu ninjutsu.
Legend has it that there was a ninja named Ikai who lived under the So regime of Korai (present day Korea) from the late tenth to early eleventh centuries. In the first year of the Kouyu era he fought a losing battle against King Jinso together with the armies of Kittan and Ka. Then he fled to Japan, landing at Ise and lived in a cave in Iga province. It was recorded that Ikai was a military commander proficient in hicho kakuregata (concealment techniques based on hicho jutsu). And it is said that he could jump many meters high with a yell. Apparantly, Ikai was the first to introduce ninjutsu to Japan.
[...] The record say that there have been seventy-three schools of ninjutsu throughout its history. Some of the main schools are as follows: Negishi ryu, Shirai ryu, Shinto ryu, and Hakuun ryu, from which such schools as Togakure ryu, Koushu ryu, Kishu ryu, Minamoto ryu, Genjitu ryu, Ryumon ryu, Tenton happo ryu and Goton Juppo ryu are said to have been derived.
Iga ryu and Koga ryu survived long enough to gain such a high reputation that they were welcomed by the Tokugawa government.
Hakuun ryu was initiated by Garyu doji and later featured the flexible usage of four demons: shadow demon, fire demon, earth demon and wind demon. During the Oho period approximately a hundred years after the Jiryaku era, Kagakure doji, who was a disciple of Hakuun doji, imparted training in ninjutsu to Togakure Daisuke, who in turn took care of Shima Kosanta. As mentioned above, there is a record that in those days quite a few survivors of the Kiso Yoshinake's army fled into the mountains if Iga province. Later on during the Engen (1336-39) and Shohei (1346-69) eras, a number of stragglers from both the South and the North Courts are said to have sneaked into the mountain of Iga and Koga provinces. Some say that this fact marks the origin of various of the ninja including Iga and Koga ryu. [...]

Taken from essence of ninjutsu by Masaaki Hatsumi.

Kukishinden Ryu
The Traditions of the Nine Demon Gods
(Sometimes written Kukishin Ryu in english)
The techniques in Kukishinden ryu are said to have come from China and the land beyond China. The Kukishinden ryu was developed in the Kumano prefecture.
During the life of the school it was employed by Japanese seamen to help protect them. This greatly influenced the schools techniques and weapons. Warriors of the Kukishinden ryu are said to have used masts and rigging during combat.
In 1330 the Japanese Emperor Go Daigo was held under house arrest at the Kazan-in, the Royal Summer Palace on Yoshino mountain, be the Shogun Ashikaga Takauji. It was Kusunoki Masashige, a high ranking samurai loyal to the Emperor who was ordered to effect a rescue attempt. Masashige had in his employment a young sixteen year old Gyoja (mountain ascetic) from Kishu, south of Nara, named Yasushimaru Kurando. Kurando was well known to be skilled in Ninjutsu and other Bujutsu arts and so was given the task of rescuing the Emperor. Aided by another samurai named Kagoshima, Kurando managed to infiltrate the Kazan in, and upon reaching the emperor disguised him [the Emperor] as a woman. Unfortunately the Ashikaga samurai were alerted when Kurando attempted to croos the "Hizume corridor" with the emperor on his back. This wooden corridor was specially designed to make loud sound as was walked on, thus alerting the guards. Kurando and the emperor were surrounded, placing the Emperor with his back against a nearby tree, Kurando faced his oncoming adversaries armed with his Naginata (halberd). One by one they attacked him, and he cut them down with his Naginata, until only their samurai officer was left. This man was a highly skilled martial artist, and as Kurando cur at him with the Naginata he retaliated by cutting the blade of the Naginata cleanly away from the shaft. Now armed only with a wooden pole, Kurando defended himself and the Emperor with a secret Rokushakubo (6th staff) technique called "Gyaku Kuji". Upon defeating the samurai officer Kurando and the Emperor Go Daigo made good their escape, and then with Kagishima he escorted the Emperor back to the capital Kyoto.

In recognition for this brave act the emperor gave Kurando permission to use the "Kuki" of Kukishinden Ryu, which suggests that he fought like "Nine Demons". Although formalised at this time, the Kukishinden Ryu has a history stretching back to the Kamakura Era (1180's), with techniques that are said to originate in China and the Lands beyond.
[...]
Kukishinden ryu hanbojutso is the main weapon taught to students of ninjutsu in the world today and is the third school in Bujinkan.
Sensei Ueshiba the founder of modern Aikido, in his youth studied the art of Kukishinden ryu Happo Hiken jutsu from the Kuki family.

Taken from "seminar notes" recieved at a seminar with Sveneric Bogsater and Brinn Morgan.

Gyokko Ryu
School of The Jewel Tiger
It is believed that a Chinese named Ibou introduced these techniques to Japan in the 8th century. According to Mr. Hatsumi that person could also be somebody from a foriegn country. It is not known exactly by whom these techniques was introduced, but it is assumed that this Kosshijutsu was developed based on Chinese Kempo. Although Kosshijutsu means to be able to knock down an enemy with a finger: it is considered that it rather denotes "the backbone (koshi): of martial arts. This Gyokko Ryu has later become the basis of various martial arts of Iga.

Taken from "Hiden Ninja Submission" by Hatsumi Masaaki.

Togakure Ryu Ninpo Taijutsu is a distant branch of the Gyokko Ryu Kosshijutsu. There is a saying in the Gyokko Ryu "Bushigokorro wo motte totosho no nasu" - 'the warriors heart is precious, and essential'.

The school specializes in techniques that involve Kosshijutsu (attacks against muscles) Shitojutsu (use of thumbs and fingers). The Ge Ryaku no Maki is the Muto Dori [(evasion techniques)] of the school and involves techniques against swords and spears. These are the most difficult and advanced within the school. Typical for the Gyokko Ryu is the powerful blocks, and balance taking. They prefer to block by hitting with the knuckles to the muscle areas.

The Nine Rules of the Gyokko Ryu