I almost believe that the Village of Konoha’s authority headed by the Third Hokage ordered the killing of the Uchiha clan’s members. This is based on the story told by Uchiha Madara to Uchiha Sasuke as told by the Naruto Manga chapter 399.
The story about the murder of the Uchihas is well said by Madara. However, just like what I said before, there’s a little contradiction on this story to what Itachi told to Sasuke. If you still remember, Itachi told Sasuke that Madara was his accomplice in killing all.
So, to whom should we believe, Madara or Itachi?
Well… I rather believe Itachi.
And I know, you’ll disagree with me. Anyway, you have points in believing that Madara was not telling lies…. consider these comments posted on my previous post, “Uchiha Madara’s Story“:





April 28th, 2008 at 7:13 pm Don;t think that Madara is actually lying. Such massacre may be against the THIRD’s principles but bear in mind the other three people - the two advisers and Danzou who handles the ANBU root division. It could have been that Itachi was in the root division. And the principles of these three living people who allegedly knows the truth are not in line with the Sandaime’s.And if Madara was lying, why would he tell Sasuke that he killed his friend and brother to obtain EMS and that he confirmed Itachi’s earlier statements that he was Itachi’s accomplice?
April 28th, 2008 at 9:24 pm Lies? I can’t really tell for sure, but in my own opinion, I don’t think that Madara is lying. Like the past chapter, all of the things he told Sasuke before are logical and fits well on the plot. And considering that Danzou is once again connected to this, everything makes sense. Again, it would probably be better to see what happens next. The plot thickens, and we’re right in the middle of it. Hot!
May 13th, 2008 at 10:07 pm Going on what Gilgy says, he has a good point about Danzou. He did give Sai the secret mission to kill Sasuke. My guess is that if Sasuke knew the truth about his clan and why they were massacred he’d turn against Konoha and Danzou knew this!!I don’t think Madara is lying, there’d be no reason too. Why would he go all the way back to the Firsts era. “It’s to in depth.” I do believe he’s trying to get Sasuke on side though.
Sasuke said it himself that he’ll kill anyone involved in the incident. Which means the main plot of this looks like Sasuke joining Akatuski and getting his true revenge against Konoha. Maybe just maybe Sasuke might become the main bad guy. An all out battle with Naruto and Sasuke looks on the cards.