Basically, the ninjas hand-to-hand fighting method was Taijutsu, sometimes referred to as koshijutsu, sometimes dakentaijutsu, or yawara, or even jujutsu. The terms changed and varied as the years went on. Sometimes it was called koshijutsu or koppojutsu or only te (literally translated as “hand”, implying “hand-to-hand”). So the basic core was Taijutsu, and after they had mastered Taijutsu they learned to employ the special weapons of their style or system. There is a theory that the fundamental base for the ninja fighting method is Gyokko Ryu Koshijutsu which was adapted in Japan from an older original Chinese fighting system. It is my feeling that this Gyokko Ryu method was not simply transplanted whole to Japan. It was absorbed and adapted to relate with the indigenous Japanese fighting methods of the period. Then this Koshijutsu (fighting method translated as “body weapon art” — koshi can relate to fingers or toes, hand or foot) was later expanded upon and evolved into the Japanese Koppojutsu (fighting method translated as “body frame art” — the body in motion breaks the enemy’s bones and knocks him down). According to Takamatsu, ninja from Iga and Koga areas mastered Koshijutsu and Koppojutsu as a part of their combat training. As you know, if you cannot properly do Taijutsu, there is no way you can do sword or spear techniques either.