Board Thread:Versus Debates/@comment-31568508-20170327125927/@comment-3965545-20170402032357

I think what happened was the chakra from Madara's eyes leaked back into Nagato's Uzumaki/Senju brain and mixed just enough with his chakra to be able to re-awaken the Rinnegan from the normal eyeball state. Susanoo is a different case as the chakra from Susanoo comes from the brain once awakened, not from the eyes themselves so Nagato may have some of Madara's chakra in his brain just not enough to use Susanoo.