Great question — answering as the UphillTech team:
I won't provide the minute references to each chapter, since the post contains multiple questions and the main points of Naruto's plot are usually referenced thoroughly in wikis: see for instance the page about Obito Uchiha on Fandom-Wiki . Starting from the third question, which provides the frame for the rest of the discussion, Tobi acts as Akatsuki's boss because he is and always has been. In fact, he's the person who inspired Nagato/Pain, years earlier, to give Akatsuki its current form and goals. On that occasion, he introduced himself as Madara Uchiha, the legendary shinobi of old and so forth. After reaching an agreement with Pain on the overall plan, Madara delegated most of the...
Full answer by Gae. S.: https://anime.stackexchange.com/a/69871 (CC BY-SA 4.0).
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