Or you could have the group of Ninjas split, thus having half captured by the Ottomans, and the other half staying in Persia. Unable to return home, they assimilate into the local society, adopt Shia Islam and open up a secret ninja school. Thus their pupils continue their legacy, but end up mixing Shia religious fervor and mysticism in it.
Voila, Persian Shia Ninjas (The Swords [or would that be nunchuks?] of Ali) - the perfect arch-enemy of the Sublime Porte's Order of most Skilled Ninjas.
Here I stand, speechless.....
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