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In Itachi's genjutsu to show Sasuke the truth of what happened, Danzo is shown with his eye patch and his arm covered. It is not clear whether or not Danzo had implanted sharingans and the 1sts cells in the right side of his arm. Perhaps he already had a deal with Orochimaru? However, it seems Obito was the one who took all the sharingans out of the eyesockets. Wouldn't the clean up crew for deceased Uchiha massacre notice these details?? Or maybe they were taken out after being put to rest.
Probably not, but Danzo's eyepatch in the flashback could also have been Shisui's eye and Danzo could have been influencing Itachi without him realizing it. However, the fact that Danzo gave Itachi to choose whether or not die with his clan or kill them shows he had a choice.
very reminiscent of Sasuke protecting Naruto during their fight with Haku. This scene may allude to Naruto powering up again (for the fight not permanent)?
also, i hope Orochimaru is the final villain, one who wishes to obtain true power through the body of the SO6P triumps any villain who only wants to control people. Had Orochimaru been able to kill the 3rd Hokage without the loss of his arms, he probably would be the strongest in the series with 3 edo-tensei'd kages in his arsenal. don't count him out yet!
my final villain theory:
He probably had already lost his eye and arm for real before the Uchiha Massacre took place, then later he decided to replace them with Orochimaru's help. His arm was made of Hashirama cells as you'll recall.
I find it hard to believe that Itachi with his great affinity for Genjutsu could be affected by anyone other than Shusui, so I doubt Danzou was affecting him. Honestly, Danzou simply reasoned with Itachi and used his love for Sasuke as leverage, nothing more, nothing less.
As for Orochimaru, he certainly has more to offer, but the as for him being the final villain? He'd need some kind of major power up, because as it stands, he lacks any real way to defend himself and is at Sasuke's mercy for the time being.