Board Thread:Naruto Discussions/@comment-24120130-20140607191120/@comment-1512913-20140701180848

"All chakra abilities had to have originated from Kaguya, because all chakra originated from Kaguya" and that is true, unless Kishi gives us another plot-twist. Since Kaguya/Ten-Tails whatever is source of all chakra and seemingly Hagoromo and Hamura each inherited a different aspect of her (just like Ashura and Indra did of Hagoromo) it stands to reason that everything Hagoromo has is also what his mother has to have. Therefore since he does have the Rinnegan, so then must she as well. There's no room for "3rd party chakra upgrade" so the only way for Hagoromo to be the originator of the Rinnegan would be if the assumed father's genes had brought a mutation.

And we don't know anything about the father or even if there was any. But scientifically, there had to be one, since the Y chromosome didn't come from nowhere, unless:
 * 1) "magic"
 * 2) Kaguya is a hermaphrodite

And since Ashura + Indra = Hagoromo, logic has it that Hagoromo + Hamura = Kaguya. Only once and if a father appears can your theory about the Sharingan having been there first work.

If Hagoromo is just 50% of Kaguya and has the Rinnegan, then she must have had the Rinnegan and more from the get-go, being the whole.