I think itachi sealed some of his spirit inside naruto. In his genjutsu he turned most of his body into crows http://www.narutocentral.com/manga.p...ruto&c=403&p=3
He then shoved a crow down naruto's throat. http://www.narutocentral.com/manga.p...ruto&c=403&p=7
. It makes perfect sense.
Sasuke is only doing what he's doing because he's trying to avenge itachi. Itachi must have known that madara would try to recruit sasuke and tell him everything about itachi's past. Therefore he implanted amaterasu in sasuke's eyes as a diversion. He must have known it wouldn't work. Madara now feels relieved that he escaped itachi's "fail safe" Itachi probable has it set up so that the next time naruto sees sasuke, itachi's crow comes back out, and transforms back into itachi. He then tells sasuke to forget about revenge, and that he doesn't want the leaf village to be destroyed. He'll then tell him that he could have refused to destroy the uchiha clan if he wanted too, so sasuke should hate him instead of the leaf. Sasuke will then finally realize that madara is using him as a tool and will forgive the senju for their actions. He and naruto then team up to take on madara
After itachi's talk, sasuke's emotions will change from revenge to justice. He'll still hold a grudge against danzo (and maybe the hokage's advisors), but he wont kill them. Likely danzo will get killed off by someone else, and the hokage's advisors will step down to get replaced by the next generation. (skikamaru and sakura)
Edit: Also it's likely that if the crow does turn back into itachi it'll have a time limit like minato. Although if itachi activated his MS during that time and gave his eyes to sasuke that would be awesome