I am bored so until I got the mood to type the actual story
Random Crack Idea:
A secret Organization that operate like M.I.B.
The Agents are nobody and remain as such.
They are not visible ninja, they are ninja whom you can't even remember.
They don't wear black suit all the time.... They only wear it depending on occasion. If you wear black suit in places where there are lots of people not wearing it and black suit have no reason to be there, it tend to leave impression...