Years of civil war have brought the ninjitsu code and its warriors to the brink of extinction. It is time to rebuild, and find the next generation of fighters who will learn the ninja traditions. A ninjitsu master stands alone amidst the wreckage of years of warfare. In his searches, he has found three children who show promise: two brothers, Kazuma and Sho, and his own daughter Aya. He begins to train them.
Fifteen years pass. The oldest boy, Kazuma, begins to reject all the ninjitsu teachings, save one: the technique of strength. Obsessed with power, Kazuma demands that the master teach him the ultimate technique which would make his power absolute. The master refuses, and Kazuma vows to return one day and take revenge. Sho and Aya continue their studies and master the ninjitsu teachings.
Now, Kazuma has returned. He has made an army and acquired the resources to build a fortress. Although the old master has died, his pupils contain within them the secrets of the ultimate technique. Kazuma sets up a trap to lure Sho into his hideout, and kidnaps Aya to use her as a bait. The fate of the world now rests within Sho's hands.
Source: Wikipedia, "http://en.wikipedia.org/wiki/Shinobi_X," available under the CC-BY-SA License.