There are two majorly conflicting camps when it comes to "ninjutsu" and I think just about any martial art when it comes down to it.
1. Tradition is defined by an unbroken lineage, and the only "authentic" martial arts MUST have a traceable lineage.
2. Martial art is defined by its effectiveness in combat. Tradition doesn't matter if the techniques can't be applied in a practical way against a fully resisting attacker.
Most "ninjutsu" would seem to fall outside of both categories. There is no fully verifiable lineage of ninjutsu out there. Even Hatsumi Sensei's is questionable. Most "taijutsu" (which really just means "body technique" so literally every martial art has taijutsu and changing the name was just a marketing technique) is either ineffective, or impractical.
...but what is a "ninja" really? Well, the words "ninja" and "ninjutsu" don't even show up until AFTER the days in which the people to which they refer were active. The word itself means something like "the art of stealth" and it was originally more about espionage than combat.
In simplest terms, ninja were just a form of early special forces, not unlike today's marines, army rangers, SAS and so forth. If you choose to reduce it down to just the combat characteristics, the original ninja would have learned budo, which in turn gave us the modern arts of judo, jujutsu (traditional Japanese), and aikido, as well as the various weapons systems of the time (naginata-do, kendo, etc).
My theory is, like modern special forces, ninja would have been given some additional, specialized combat training. Because they would commonly be deployed singly, or in small units, and their missions were more intellegence gathering than full-scale combat, the focus would be more on quick neutralization and escape.
This is actually very practical in modern application of "self-defense" because we will not have a full garrison at our backs when attacked, and our job is to create a window and get out as quickly and efficiently as possible.
So, ninjutsu CAN be practical, but we can't depend on an unbroken lineage, so we have to focus instead on combat effectiveness.
Keeping as true to the original model as possible, the methods should be as direct and efficient as possible. So "economy of motion" should be a key principle. In addition, because we know they learned budo, we can look to their offspring- aikido, jujutsu, and judo, for inspiration and techniques.
I shouldn't have to make the case that kyushojitsu is present in jujutsu, and aikido's atemi waza. Suffice to say anyone properly educated in these schools will know immediately, unless they are deluding themselves, or are woefully misinformed as to what kyusho really is.
Add to that some escape and evasion techniques, maybe a few concealable and improvised weapons, and you have yourself a functional modern ninjutsu system.
Before my transition, I founded a system I called "Hatchie-Ryu Ninpo" based on my personal experience, and things I had learned over the years. I wrote a book which you can find HERE on Amazon.
From my 2 years living in the wilderness I drew stealth and survival techniques. From my training in aikido and kung fu I drew throws, grappling, and the fundamental principles of power through "softness" and blending. From my experience with real-world self defense, I drew my efficiency, and more direct approach than I learned from any formal training. Kyushojitsu was a big part of this.
It is my belief that kyusho was always a part of traditional Japanese martial arts, and that it would have been emphasized in the training of special operatives of the time. Applied correctly, it imparts a significant edge against a physically superior attacker. This makes for a much more effective and efficient neutralization of threat. There are certain principles which must be taught in person, such as flowing movement and chaining attacks, not to mention all the elements of internal power and blending. Nonetheless, I consider a foundational knowledge and understanding of kyushojitsu to be critical to the would-be modern "ninja"
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Born intersex, assigned "male" at birth, but her femininity was obvious as she developed. Ergo, Rae is both "intersex" and "transgender" in that her gender does not match that assigned at birth. She identifies as "hijra" or "kathoey" -words from Hindi and Thai languages respectively for "third gender" people. Rae is an author, holistic healer, and martial artist. She teaches and provides services professionally.