Originally Posted by Fenrii
The only think I think the eyes meant at all was that he was about to lose it. Every time he gets really emotional he sprouts tails and loses it. Nagato just forced him to re-live J-man and Kakashi's death so I am pretty sure he would be very emotional at that point. I think because he was in sage mode and recently had the seal strengthened he was able to keep from losing himself, but Kishi showed us the fox/sage eyes to let us know just how close he came to going fox again after seeing that.
I also think it's just the emo state Naruto is in.
My prediction is in next chapter Nagato kills the Konoha shinobis using his rinnegan ha...power. That will also be another scar on Nagato because he never wanted to hurt anyone. Then after that he will go around alone until he meets Yahiko and Konan. They will struggle to survive until they meet Jiraiya. But after Jiraiya leaves things will start going bad again. So Nagato, Yahiko and Konan will form a team and do some active things on their own. After Yahiko dies Nagato will turn that team into akatsuki. Maybe the whole story will last for two chapters.