Contradicting to their beliefs, Ninjas are in ways just a fancier word for Spies. In short they are for hire, mercenaries. They spy, sought information, sabotage, hide in disguise, and of course assassination. No true ninja ever wants to be revealed, else how can they perform their impossible mission if people knew their names or what they look like. In history the best Ninjas are never known because that's a Ninja's true path. Much like a Samurai's "Way of the Warrior", Bushido. Of course people have their own ideals and beliefs and to this day that hasn't change either.
Samurai's are not all good doers that follow by the Bushido code. Ninjas are the same way. They will fight dirty, cheat, and do anything to gain the advantage in a fight. Mostly to flee and not do battle. They do this in history because they are often have inferior equipment, when compared to an armed Samurai, plus they need to travel lightly. Of course there are more than one type of ninjas and some ninjas do excel in combat arts.
One of my favorites Ninja stories involves Yukumara Sanada, a samurai, during the Sengoku Warring Period. It says in legend that Yukumara was invincible during battles and would often be "unharmed". Some speculate that the source of his "invincibility" was because he secretly had a Ninja that aid him in battle. And many times he would escape "impossible scenarios" with this ninja's help. This Ninja's was never known or if existed at all.
Blah, blah, blah enough of a history lesson and what I known cuz I ain't got the reference for it anyways (it's been a long time since I read up on those). More or less this is a fictional story and you can make them do whatever you want them to do. TBH, if you don't know what direction you want to head in then chance are I can't help you much because this is your story. I'll gladly help you out, but I won't dictate the tempo.
IMO, I'd say you should scratch the whole story. Yeah, I know what your thinking. But sometimes when your stuck in a BIG rut like you are now where your clueless. The best thing to do is rewrite your whole story and re-imagine everything. You might just find the answers to your questions or you might create something even better. I've done this before so I can ensure you it does yield promising results.
My 2 cents. Based on some of the information you'd provide I feel that you could drop the whole "Ninja Theme" all together. Perhaps approach more of a "Summoner" sort of theme. Like Card Captor or Fate Stay/Night if you need a reference. If your keen on keeping your original format then I'll need a story synopsis to paint a clearer picture of what I'm working with here.
Let me know what you think and I'll get back to you.