The story I've found about how Tanemura-Soke left the Bujinkan, (in a nutshell)... thought it was a fascinating bit of Ninpo history that you may enjoy.

Hatsumi Yoshiaki (Masa-aki / Byakuryu) Former-Teacher of Shoto Tanemura. Tanemura Shoto (Tsunehisa) was training Takamatsu in martial arts from April of 1963 (15 years old) to November of 1984 (37 years old) under Hatsumi Yoshiaki (given name), the president of Bujinkan Dojo and President of Bujinkan Shidoshi Association. At the time, Tanemura was also the Vice President of the Bujinkan Shidoshi Association. In March 1984, one of Tanemura’s highest ranked students had to resi
gn and dropout from Tanemura’s Dojo and the Bujinkan Shidoshi Association, because of serious problems he had caused. On the 1st of November 1984, Tanemura found out that Hatsumi had taken care of this problem student, without Tanemura’s knowledge. There were many reasons for Tanemura’s decision to leave Hatsumi but the final decision to separate was a result of being disappointed by Hatsumi’s decision to look after this problem student. Tanemura decided on the 13th November 1984 to resign from Hatsumi and the Bujinkan Shidoshi Association. On that day Tanemura sent a letter by registered post to his teacher Hatsumi, explaining his reasons for resigning and his wish to become independent. Tanemura went on to establish the Genbukan Ninpo Bugei Dojo on November 28th, 1984. He started teaching the Takamatsu Budo that he had mastered and been given Menkyo Kaiden from his former teacher Hatsumi, as Tanemura-Ha. Tanemura decided that he will preserve the true spirit and teachings of Takamatsu as Tanemura-Ha (Tanemura-line). This was a very hard and sad time for Tanemura to leave Hatsumi. However, it was important for Tanemura to follow his heart and keep alive the martial arts of Takamatsu. After leaving Hatsumi, Tanemura was fortunate to learn and receive Grandmasterships and Masterships from Takamatsu’s highest ranked students; Kimura Masaji, Sato Kinbei and Ueno Takashi’s line Masters. He has also learned from many other Grandmasters/Masters of different types of Ryu-Ha and martial arts. And he has received many other Grandmasterships/Masterships.