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A plot ninja is something that is inserted into the plot when the writer finds him- or herself at a loss for what to do next, or when their characters are bogging down in dull conversation rather than doing anything interesting. The traditional form of the plot ninja is literal ninjas crashing through windows or leaping out of wardrobes and attacking the main characters, turning the dithering over plot into an exciting action scene. When actual ninjas are not appropriate, milieu-appropriate enemies, such as orcs, cyborgs, or gangster can be substituted.
In a more general sense, a plot ninja is any plot element, perhaps randomly generated or taken from other's suggestions (such as dares), which a writer will toss into the story when things are slowing down.
Compare to the Busty Lesbian Cabbage Pirate Ninja, an early NaNo variant of the plot ninja.
The plot ninja is not to be confused with the plot bunny, despite their similar names.