Real Ninjas were just assassins, like assassins in any culture.
Only the use of Oriental Martial Arts and Weapons made them exotic to foreign cultures like the US and post WWII Japan. (I put this as a foriegn culture compared to pre-westernized Japan)
Ninjitsu proponents will try to tell you that Ninjas have a long history in Japan…but what we would consider a ninja only existed for a short period - the age when the Samurai were being disempowered. Then you have highly trained combatants available to nefarious purposes. This was a notably brief period of time, possibly as long as 5-10 years. I doubt the word Ninja (or Ninjitsu) was ever used in that time.
Prior to that time, there were assassins, but the majority of these were no more sophisticated than the average mob hit man.
Proponents of Ninjitsu will cite records such as Togakure-ryū, but these records are mostly considered to be manufactured history.
Most of what you consider a Ninja is purely hollywood. Oriental Assassins were only considered mystical because of their exotic foreign nature.
For a real look at a mysterious cult of assassins, do some research on the Hashasheen of the arab world.