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Yes, I know. Madara may have controlled Yagura to begin with, but before or after he died Tobi/Obito took over. Tobi then revealed himself to Kisame claiming to be Uchiha Madara 16-13 Years ago give or take.
My working theory about Madara/Obito/Tobi is this: Madara lived in seclusion after Hashirama shoved a sword through his chest studying his cells in order to recreate the Rinnegan and move his own plans forward. Around 30 years ago give or take Madara brought Yagura under his control and began the Bloody Mist era.
At some pont Madara's experiments with Hashirama's cells resulted in Zetsu's creation, and he used him to keep track of his enemies. He probably had Zetzu snooping around in Konoha quite a bit.
Now as for Obito...I think it's very likely that he is related to Madara, given how similar they appear. This is also important because it explains why Madara, in this scenario, would bother with a half-dead canon-fodder shinobi like Obito appeared to be at the time. He is his descendant. So...He sets Zetsu to observe Obito or others he believes may be useful to his plans, and when Obito is left half-dead Zetsu retrieves him.
Madara then proceeds to patch Obito back together, somehow brings him around to his way of thinking, and begins to train him. Sometime during this period, Madara finally awakens the Rinnegan. Unfortunately for him, Tobi gets ambitious and decides to kill Madara and take the Rinnegan for himself. Tobi succeeds in killing him, but Madara pulls a Danzo and crushes the eyes before he can get his hands on them.
Sometime before or after this, Tobi picks up where his predecessor left off and takes control of Yagura for his own purposes, and reveals himself to Kisame claiming to be Madara.
Then...we have the Nine-Tails' attack. Bam.
The advantages of this theory: It solves most of the issues with Tobito, and it explains something that has been bugging me for a while now; how Madara died. Tobi killing him and taking his place would be a bit poetic IMO.
Hmm, an interesting theory that we'll have to consider xd
However, it doesn't explain how Long-Haired Tobi made a comeback at the Uchiha Massacre which occurred after the attack on the village.