In the twelfth century, a samurai named Daisuke Nishina suffered a crushing military defeat. Rather than face his death like a man (pfft!), he fled into the mountains, and that's where things get hazy. Some say he met a wise man from India, some say he met a monk from China, some say he met a tengu - but in the following years, a new breed of warrior arose in Japan. Unbound by the principles of bushido, these unconventional warriors eventually came to be known as ninja. They fought uncommonly well, but "dirty" (to the samurai), using techniques that exploited principles of leverage and body mechanics without relying so much on strength or speed. They also engaged in psychological warfare as their legend grew, cultivating their own myth to their advantage and pressing it against their superstitious opponents. And, of course, they used stealth - skulking about in the dark, striking from the shadows, disguising themselves, and various other "dishonorable" tactics that would be unthinkable for a samurai.
That thing I mentioned, about Japanese being more suggestive than explicit - that applies to the word "ninja" as well. It's composed of two parts, "nin" and "jin." Jin, simply, means person - nin, however, not only means silent/stealthy/invisible, but also persevering. That alone should give you great meditation fodder for at least a couple hours, if you didn't know it already (or maybe that was just me?). This multiplicity of meaning is also borne out in the art itself. Here is a man demonstrating some basic techniques:
Wait, why is he teaching how to be a ninja for free online?
They don't look very deadly all on their own. They're not, in fact, because that's not what you would do in a fight. Those techniques aren't "moves," they're more like "notes." You know how good notes boil down the essence of a lecture, even though the lecture itself is tailored to the students present at the time? So it is with using Bujinkan in a fight: you remember the techniques, and perhaps go through motions very much like them, but in the end the specifics of your movements are determined not by rote memorization but by applying the general idea to your opponent in the moment. Here you can see those same techniques, but demonstrated with a partner to show a few of the different ways you can go (he even touches briefly on the fact that every technique has an inside and an outside, when discussing the difference between sui no kata and ka no kata):
I swear, any second, assassins will cut him down for spilling the beans...
Incidentally, this is why the scrolls - yes, there are real ninja scrolls - are useless to the uninitiated. They're notes, not explanations, and the real meat of the technique is handed down through tradition. Now, almost any martial artist will tell you that of course you have to tailor your technique to your specific opponent in the moment - I mean, duh, that's just common sense! But that's just the thing - traditionally, martial arts were taught by rote, and masters would know what technique to use and when by simple muscle memory. It was a matter of having enough moves and the practice to apply them properly. Bujinkan turns that upside-down, teaching instead that everything is a stance. However you could possibly stand, there is some conceivable circumstance where that would be "the thing to do at the time," so you must be open to it. The forms are inspiration, a starting point - the art itself is formlessness, nearly a thousand years before Bruce Lee invented Jeet Kune Do.
Takamatsu was the last grandmaster of the order to actually assassinate people, and his life is also the stuff of legend. At twelve, he was jumped by five guys with swords trying to kill him. As he walked away, having killed them all with his bare hands, he felt something sticky on his pinky - he looked down and was startled to see an eyeball. Don't believe me? Look at his hands:
The deadliest old man hands you will ever see.
Those suckers could strip the bark from a tree in a few effortless swipes. He'd beat sumo wrestlers - at sumo wrestling. Even in his old age, he was feared - when he heard that the Yakuza were muscling in on the businesses of some of his friends, he walked the fuck on up and told them to back off. And the Yakuza listened. He practiced every single day until the day he died, and was only once seen to take a knee - the day before.
He eventually passed the title of Grandmaster down to Masaaki Hatsumi, who has since "gone public" with the art, presumably so that it won't die in secrecy. When Takamatsu died, even his close friends didn't know he was the grandmaster of the nine schools until they read it in his obituary.
Of course, Bujinkan has been covered on Human Weapon, a wonderful show where two guys go around the world taking crash courses in various martial arts and getting their asses handed to them. Irritatingly, they call it "ninjitsu" at every turn - "jitsu" means "truth," "jutsu" means "technique." Jerks. But it's worth a little gaijin jackassery to see these guys go toe-to-toe with some hand-picked students. I mean, sure, they score a few "points" against their opponents during the final showdown segment - but watch what happens one of the students hits one of the stars in the head (it's near the end, skip to 39:45 if you wanna jump right there):
Learn an ancient, secret art in a week? Dude, I got this.
Bruce, the student, asks Bill if he's all right - but Yost waves him off with gentle reproach. If you watch the whole episode, you'll get a sense for Yost's subdued manner. The message is clear: "You damned fool! These are friggin' actors, you should have more self-control!" Silly ninja, letting a teevee contest get to his head...