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Originally Posted by Sabaku Kyu
Not to mention it's really confusing why Pein follows Madara if he possesses "the greatest of the three great doujutsu"
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We saw only one eye of Madara's current body, and seeing how cyborg-esque his outfit is it may be that his other eye is like Pein's eye. It was already made clear that bloodline powers are almost always beaten by great genious ninja. So having the eye or whatever will not grant victory. Why Madara is the strongest of all must be not only the eye but also his talent and the hundred years of expreience. Kakashi just by having 1 eye could copy a 1000 jutsu, just imagine someone like Madara how many jutsu can copy over a 100 year's time. He was already a legend when Pein was not even born.
I just remembered some of Itachi's speech, where he says something about "testing his container", this might be connected to the soul transmigration thing. If Itachi did not destroy his own clan than it was either Madara or Pein by posessing his body and using his abilites to kill all the Uchiha. In that case Itachi was just a puppet. It was in anime, maybe was a wrong translation.
Other interesting thing is that in episode 131 Itachi says to little Sasuke to obtain MS by killing his best friend, and come to him only after he has the MS. In present time however Itachi didn't say to Sasuke to not come after him until he does not have the MS, he didn't say anything. One would expect a speech from Itachi, where he says that Sasuke is still weak and that without MS he is nothing. But nothing was said, maybe Itachi said all that to Naruto, who didn't understand anything of it? Itachi inviting Sasuke to a secret meeting could be an indication that he and Madara are connected, because Madara was satisfied with Sasuke's performance against Deidara, and in that case he would tell Itachi to not care that Sasuke does not have MS and invite him anyway.