Board Thread:Naruto Discussions/@comment-25442710-20140920121351/@comment-3568954-20141006021144

ItachiWasAHero wrote: Obito at least should have awakened his own Rinnegan. This also explains Nagato's power and proficiency with the Rinnegan and why he was Edo Tensei's with eyeballs that were not his. Itachi was blind at death, yet was Edo Tensei's with full eyesight and his own eyes, even though Sasuke had his eyes. So it makes me think that Nagato did indeed awaken his own Rinnegan, using Madara's Rinnegan. It now makes sense as to why Obito called him the 3rd Sage of Six Paths and called Madara the 2nd Sage of Six Paths..

It is my theory that the reason Nagato still had them was because all though Nagato had transplanted Rinnegan they were not active until after he had experienced pain so he essentially actually awakened them. either that or Maybe Madara did not actually transplant the actual eyes but maybe he removed the very essence of the Rinnegan from his body and transplanted it into a baby nagato as in he gave him his cells which were bound with Indra and Asura's power or something like that