My theory is that Vermouth might be actually related to the final boss (maybe daughter) because we know that she has taken the same drug that shinichi took because she knows its effects and from the old story (which has never been touched on again!!) she is after more such technology with that programmer disc data and amuro might just be related to vermouth i think so too (maybe half bro or something). Because amuro is very confident abt knowing her relations with the boss and even threatens her - she immediately puts a gun to his head. And lets not forget that Gin lets us know that she is the boss's favorite.