<p>If it helps clear anything up, here's everything we know about Kaguya being the Ten-Tails in the manga:
</p><p>In chapter 681, Naruto is suprised when Black Zetsu says the Ōtsutsuki brothers used their seal on Kaguya, since he was told they used it on the Ten-Tails. We then get the truth revealed:
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<div class="quote"><i>Black Zetsu: First off, Ten-Tails... is not just the God Tree... It is Mother herself, as well.</i></div>
<p>But then he starts talking about how the Ten-Tails was following Kaguya's will, leaving it unclear whether she actually was the beast or simply created it. However, the fourth databook's shinobi compendium clears it up:
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<div class="quote"><i>"Devising a plan to absorb their chakra, [Kaguya] integrated with the God Tree and challenged the twins to battle... The twins, assuming that Ten-Tails was an incarnation of the God Tree, and that it had attacked them to recover the chakra from its stolen fruit, met it head on. After a desperate struggle, they invoked Six Paths Chibaku Tensei. Transforming it into the moon, they sealed it away."</i></div>
<p>This backs up what Black Zetsu says in the manga. After he reveals that the Ten-Tails was trying to reclaim all chakra for Kaguya, he says that even Hagoromo himself was unaware of this fact, which would be impossible if he saw Kaguya create the Ten-Tails like he did in the anime. The anime's writers apparently noticed this problem too, because they slightly altered Black Zetsu's dialogue so he doesn't say this part. They also added extra dialogue where Sasuke says Hagoromo must have known his mother would return, but then... why wouldn't he just tell them that? There's no reason for him to hide the truth and pretend Ten-Tails was just the God Tree if he knew better.
</p><p>The other key piece of evidence that Kaguya actually is the Ten-Tails is how she was revived in the first place. Apparently, the only way to revive her is to restore the Ten-Tails and then have it absorb an enormous amount of chakra, allowing her to turn back, which would be weird if the Ten-Tails was a completely separate being. Plus, when she turns into the unstable rabbit Ten-Tails, Black Zetsu is surprised because it wasn't a willing transformation, implying she has willingly become the Ten-Tails at least once before. There's also the fact that the anime shows Kaguya getting sealed in the moon rather than the Ten-Tails, but then in the present the beast's husk is somehow in there instead.
</p><p>It's easy to see how the anime writers got things mixed up, since this information is presented in such a confusing manner, but it's also important to remember that those Kaguya episodes were filled with tons of other mistakes as well, including really obvious stuff like Hagoromo creating the tailed beasts before Asura was born and toads somehow using Water Release before they even had chakra.
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