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As far as we know, Kakashi is not related to the sage in anyway (Not Uchiha, Senju, or Uzumaki) but he was still able to use the MS proficiently as many Uchihas (Sasuke, Obito, and someone as awesome as Itachi) have commented. It wouldn't be that far-fetched for Naruto to use some sort of Doujitsu. We have seen him with weird patterns in his eyes already (Sennin Mode /+ Kyuubi). I don't know what it is but I keep thinking Sasuke will make a 180 turn around and save Naruto while suffering from a hole in the chest then plucking his eyes out and telling Sakura (who happens to have a M.D. in Narutoverse) to transplant them making Naruto go OMGWTFBBQ on a Madara turned Devil-like-God-cotton candy-Super Saiyan-Chuck Norris.
And it wouldn't be too difficult to turn Sasuke good again. It's as simple as Madara saying to Sasuke "I'm the one who convinced Danzo to convince Itachi to massacre the Uchiha Clan because I can, it's fun, and my eye's put Itachi's Tsukiyomi/Amatsukami to shame."
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