The real Naruto is hiding somewhere and just a hypothetical thought what if Naruto learned to finally master Sage Mode during this time. Remember when Naruto trained with the frogs and discovered after training that he couldn't fully go into the Sage mode without Naruto's other abilities of S-Class Clones and learned how to do it without anyone's help. He was never synced with the 9tails(Karama) to actually stay in the mode for only about 15 minutes just think about it he's now synced with Karama he should be able to go into Sage Mode alone with using the 9tails charka. Even the Manga when Naruto fought the 3rd Raikage he wasn't synced with the the 9tails and could only switch between modes. I think the real Naruto has/will awaken the powers of the Sage of Six Paths when all said and done.