Pain seems to know quite a bit about Sage mode. I didn't expect that.
I think he knows that you can only gather it when you don't move. Now that Naruto is out of Sage mode he'll think that he won't be that hard to deal with (which is still true no matter how much Naruto has progressed) if you don't give him time to gather nature chakra. So he'll send in fatty Pain to deal with him. Then Naruto will show us the trick he came up with to gather nature chakra while moving and beat that Pain too.
But the second Sage mode will probably last even shorter than this one and it won't be enough to defeat the last path of Pain.
Naruto will either run of of it just after beating fatty or shortly before he could defeat the last path and it'll leave him heavily drained.
I can't decide yet if he somehow beats that Pain too, get's saved by someone else or will be defeated and possibly taken.
And what the hell is that stupid Danzou waiting for. How will he and his roots troop look like the hero of the day now. Claim Narutos actions as his own? He missed the moment if you ask me.
"For Feanor was made the mightiest in all parts of body and mind, in valour, in endurance, in beauty, in understanding, in skill, in strength and subtlety alike, of all the Children of Illuvatar, and a bright flame was in him"