Lol, special seal and it would take 3 years. You're trying to make a some kind of horror over this. What could Kakashi and Kankuro do against all of the people. The manga would completely lose its sense then.
The only FanFic idea I have takes place during the first ninja war.This kind of sounded like a mix between Naruto, Terminator (Future timeline) and Lord of The rings. Add a little Star Wars and you sir are completeFanFiction idea?
Time-skip and Madara breaking free are the only things I believe will happen though.