A ninja is a (typically Japanese) warrior, trained in martial arts fighting styles, and whom typically specializes in stealthy tactics and unorthodox arts of war.
Though it is difficult to determine much of the Ninja's history, they were first mentioned in historical documents in the 14th century, though it is widely believed that Ninja existed in secret for many years prior to being publicly known.Ninja acted less as the figures shrouded in black that most picture, and more as plain clothed scouts, noting their adversaries strengths and weaknesses in the guise of civillians before striking. Ninja were often mercenaries hired by a person or group who they hold no loyalty to after the completion of their task. Ninja are ruthless fighters, and are known to fight very dirty, and use tactics such as throwing shards of broken glass into their opponents eyes to disorientate an adversary before dealing a fatal blow. Unlike Samurai who were honor bound warriors that followed a strict code, and shunned Gaijin from joining, ninja had no strict honor code and were known to welcome outsiders who proved worthy, and able to further the goals of a clan. Ninja were in a way, the Mafia of ancient Japan, and were possibly the most ruthless warriors in history.
Ninja are all trained in the martial art style Ninjutsu, one of the deadliest Martial Arts, so much so that in many countries and regions it is actually illegal to teach in modern times. This style also teaches an amazing stealth technique that is so effective a ninja who has mastered it fully can literally remain hidden from someone they are standing in front of. Though it is in honesty difficult to decipher fact and fiction when it comes to this mysterious order of assassins who originated in Japan.... The only undisputed fact about the ninja are that if you cross one, you are likely going to die.
Ninja are a real world concept applied in numerous anime and manga, it is unknown who first started the Ninja clans and thus it is not appropriate to assign a creator or history of creation to this concept until historical documents are found that change this fact.
Ninja first became popular in mainstream media in the late 60's and 70's, often seen in martial arts movies featuring actors such as Bruce Lee and Chuck Norris as cannon fodder henchmen for the films protagonist to defeat in large numbers. In the 1980's Ninja became a household phrase thanks to the comic book/cartoon Teenage Mutant Ninja Turtles. In modern times the franchise Naruto has become the most recognizable user of the ninja concept, and perhaps the most accurate in the sense that the ninja are often paid mercenaries, The show G.I. Joe Renegades has also explored the criminal aspect of ninja in some of it's episodes, as well as containing a ninja protagonist in it's cast of characters with Snake Eyes.
Ninja appear in numerous series and franchises, and corresponding story arcs related to them. These include but are not limited to: