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I think that when Kaguya died, her chakara transmigrated back into the shinju itself (or the juubi if she died while it was in beast mode). More specifically, her chakara transmigrated into the body of the juubi. As a result, when Hagoromo split up the bijuus, Kaguya's chakara stayed inside of the gedou mazou and got hurled up to the moon.
When Madara awakened the rinnegan centuries later, he unlocked and summoned the gedou mazou from the moon and connected to it using its chakara as a life support system. At this point, I believe that some of Kaguya's chakara flowed into Madara from the mazou. As a result, when Madara created Black Zetsu, he actually injected Kaguya's will onto Zetsu.
This theory is further supported by the sillohette of Kaguya's eyes inside of the shinju.
Now you may be wondering: "Why didn't this affect Obito when he connected to the juubi and when he became the 10 tails jinchuuriki? Why didn't this affect Nagato when he connected to the mazou?"
Answer: Nagato and Obito were not Kaguya's chosen ones. It was Madara. Kaguya wanted to envelop and take over Madara's body so that she could be at full power when she returned. Nagato and Obito were not transmigrants and therefore could not awaken the shinju eye. They were not the original awakeners of the rinnegan. Obito wasn't even able to handle two rinnegan let alone the full power of Kaguya. Nagato also had his own plans and wasn't really going the route of infinite tsukuyomi.
Kaguya knew that Madara however, shared her ideology (at least to the extent of doing infinite tsukuyomi) and that his body would be able to handle her power. That is why Kaguya chose Madara. That is also why Kaguya tried to rip Obito's consciousness apart and escape his body when Obito became the 10 tails jinchuuriki while Madara was able to handle it from the start.
What do you guys think?
When Madara awakened the rinnegan centuries later, he unlocked and summoned the gedou mazou from the moon and connected to it using its chakara as a life support system. At this point, I believe that some of Kaguya's chakara flowed into Madara from the mazou. As a result, when Madara created Black Zetsu, he actually injected Kaguya's will onto Zetsu.
This theory is further supported by the sillohette of Kaguya's eyes inside of the shinju.
Now you may be wondering: "Why didn't this affect Obito when he connected to the juubi and when he became the 10 tails jinchuuriki? Why didn't this affect Nagato when he connected to the mazou?"
Answer: Nagato and Obito were not Kaguya's chosen ones. It was Madara. Kaguya wanted to envelop and take over Madara's body so that she could be at full power when she returned. Nagato and Obito were not transmigrants and therefore could not awaken the shinju eye. They were not the original awakeners of the rinnegan. Obito wasn't even able to handle two rinnegan let alone the full power of Kaguya. Nagato also had his own plans and wasn't really going the route of infinite tsukuyomi.
Kaguya knew that Madara however, shared her ideology (at least to the extent of doing infinite tsukuyomi) and that his body would be able to handle her power. That is why Kaguya chose Madara. That is also why Kaguya tried to rip Obito's consciousness apart and escape his body when Obito became the 10 tails jinchuuriki while Madara was able to handle it from the start.
What do you guys think?