A ninja is an assassin whose origins are Japanese. They were used as a threating tool by various rulers. When they were no longer useful, they were disposed of quietly, thus the mystery shrouding the ninja legend.
Of course, the current conception of ninjas is one that is far more facinating. The history of the current ninjas would not easily be put into one page, seeing as there are so many different ideas relating to the ninja. Two of the more notable ones are "Teenaged Mutant Ninja Turtles" and "Naruto."