This will be completely separate to the Original Naruto series and Shippuden. Almost in a different dimension.
Introduction:
The moon is high in flight above the Metropolis; Konoha and somewhere deep in the concrete jungle, outside the boundaries of law a cruel fate awaits an innocent victim. The fear sends adrenaline pumping through her veins as she gasps for air sprinting down the street and in a frantic panic, her mind leads her down a dead end. Spinning around to attempt to escape the way she came, she is met with the realisation it is already too late. Two men, in all black block her path. The cause of her fear. She dreads the calm before the storm, as the men slowly close in on their prey and just as all hope had left her heart. A shadow from behind one of the men suddenly becomes a man itself and dispatched one of the men with a blow to the neck. As the other turned around to attack. The third man quickly grabbed him by the throat and lifted him off the ground, clenching the mans neck tightly. "You feel that fear? That helplessness? It's horrible isn't it? So why wish it on another?" The third man speaks. He is dressed in black himself but is wearing an old fashion Japanese Fox Mask with a long trail of white hair down his back. He thrusts the man against the alley wall, pausing for a moment and then takes his leave. "Wait! Aren't you a Shinobi like them?" The woman cries out to the third man confused. "What would have happened if I had done nothing? It is not about who is or isn't. That is too shallow a thought process for me to stomach." He replies. "Th-Thank you. If there is anything I could ever do to replay you. You need only ask." The woman confesses. "Your courage is enough." The man says before disappearing.
This is not how the relationship between our characters will start. This is an encounter with a different woman just so you can get a vibe for the over all plot.
Side Note:
Sorry if my writing seems rushed. This is the first time I've put this idea down on any form of virtual paper. I would love to answer any questions and any criticism is always welcome.