
I don't know a whole lot of depth about the ninja lore since I only ran through the 30-50 quests once, but sure why not? There's only one small snag, maybe, that I could think of.
The timeline for how things in Doma is, to my unaware mind, not entirely rooted out yet. We know Doma got razed recently, as part of the backlash of the rebellion, but we don't know when that actually started (do we?) If your Master went to Eorzea to hide in the wake of it, your pupils had, at best, a couple of months of training before everything caught up them. Might smooth out a bit better if the master simply retired and left to walk the earth, Kung Fu style, perhaps knowing that there would be turbulence ahead. The Garleans took him out simply because they knew his name and he was a loose end, etcetera.
Your story, though. Looks fine to me.
The timeline for how things in Doma is, to my unaware mind, not entirely rooted out yet. We know Doma got razed recently, as part of the backlash of the rebellion, but we don't know when that actually started (do we?) If your Master went to Eorzea to hide in the wake of it, your pupils had, at best, a couple of months of training before everything caught up them. Might smooth out a bit better if the master simply retired and left to walk the earth, Kung Fu style, perhaps knowing that there would be turbulence ahead. The Garleans took him out simply because they knew his name and he was a loose end, etcetera.
Your story, though. Looks fine to me.