We know that from the Juubi's point of view, it saw the Bijuus' chakras inside Naruto:
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But another peculiarity was that the Juubi saw Rikudou's image in Naruto:
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Which made the Juubi visibly distraught:
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That same imagery of Rikudou appearing in Naruto mirrors that of when Nagato's Chakra flowed into Naruto when he was stabbed by Pein's chakra rod:
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Like I've hypothesized before:
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The Rikudou Sennin's Chakra essence is sealed inside the Bijuus (much like Minato and Kushina's chakra were inside Naruto)
That aside from Naruto receiving the Chakra of the Bijuus:
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Naruto also acquired Rikudou Sennin's Chakra sealed inside the Bijuus (The same Uzumaki Fuuinjutsu Kushina and Minato used to seal their chakra essences inside Naruto)
Even Tobi/Obito realized that there is something different in Naruto and not because of the powerup the Bijuus gave him:
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I think it is only a matter of time before Rikudou Sennin completely manifests inside Naruto, possibly when he receives the Yin Half of Kurama's Chakra Rikudou will finally emerge.
