The most reliable reconstructions of ninja history suggest that ninja denotes a function, not a special kind of warrior — ninja WERE samurai (a term, which didn't designate a class until the Tokugawa period—AFTER the warfare of the late medieval period had ended—before that it designated only an occupation) performing ninja work.
Movie-style ninja, BTW, have a much longer history than the movies (although the term ninja does not appear to have been popularized until the 20th century). Ninja shows, ninja houses (sort of like American haunted houses at carnivals), and ninja novels and stories were popular by the middle of the Tokugawa period. The ninja performers may have created the genre completely out of whole cloth, or they may have built on genuine lore derived from old spymasters. Either way, however, its clear that much of the lore underlying both modern ninja movies and modern ninja schools has both a long history AND little basis in reality outside the theatre.Not only that, but someone else claims in the comments that the black costume traditionally associated with the ninja was actually derived from the costumes worn by Japanese puppeteers working on darkened stages unseen, and not from any sort of martial tradition.
I guess this settles the whole pirates-vs.-ninja gedankenexperiment then.
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