As I stated previously, Naruto could be elsewhere like in some other dimension with Sasuke, where they would be making out (jk).
Or he could be away on a Gokage summit. There are numerous possibilities. But, I personally feel it might be related to Ōtsutsuki clan somehow. So, the other dimension is my best guess. There is a big clue that is hinting towards the involvement of the Ōtsutsuki clan in whole thing.