what's so difficult to understand ?what do you mean by black zetsu's eyes?! I questioned Kishi's logic of making a return of Kaguya!
we learned that kaguya was part of the 10 tails.
the 10 tails was sealed in the moon
madara summoned the 10 tails/ which is also part kagyua.
madara put everyone into IT so that he can steal there chakra [that's why that one panel showed he was touching the ground]
we later learn that black zetsu is the actual will of kaguya. basically they both are the same
and so black zetsu took control over the already two rinnegan,juubi jin,third eye madara. and then he took the chakra from all the ninja's caught in the IT, and since he was the will of kaguya he manage to brought her back the way she was in the past.