In every form of fiction who would you say is the greatest ninja of all time? As you can tell by my avatar you my vote goes to Master Splinter.
@Jonny_Anonymous: Thats the beauty in the semi-fiction part. He's rumored to have also been a vicious ninja from his association with the Iga and Koga clans. Legend even says he united the clans under an alliance kept secret to prevent disputes but save their pride. And he may have had several aliases/allowed people use his or faked the death of one if he needed to move on.
@Jorgevy: Who's Shedinja?
ninjask's alternate evolution (even though it's more of a collateral damage evolution, not exactly alternate since you can't choose between the two, you automatically get the two if the conditions are met)
The Grand Master of Lin Kuei clan, Sub-Zero.
I thought Sub-Zero said he wasn't a ninja?
Yes, he said that IIRC, but not because he wasn't a ninja. He was just so loyal. "I am not a ninja, I am the fighter of the Lin Kuei clan"