Board Thread:Naruto Discussions/@comment-3279282-20140828133937/@comment-4912646-20140829024129

The (presumably dropped) Bloody Mist subplot is still a giant mystery we may or may not ever get answers for. What we know for facts:

So it was probably both controlling Yagura at different times, but Obito somehow didn't know that Madara had done so before him.
 * The Bloody Mist was started by the Fourth Mizukage, according to the Fifth.
 * It started sometime before Zabuza's graduation exam (and before Obito became Madara's successor).
 * Yagura was controlled with an unknown genjutsu by a person identifying as Madara.
 * Ao saw through the genjutsu, Yagura somehow died, and Isobu was released into the wild.
 * Kisame worked for the so-called "Madara". He later identified Obito as "Madara" upon seeing his real face.
 * Kisame apparently joined Akatsuki without knowing Obito was involved (coincidence I guess?).
 * The real Madara also somehow controlled Mist ninja in the past, seemingly without Obito ever realising.