Greetings, Naruto readers! I think it is time to unravel the mystery of the Uchiha massacre. We have now enough hard facts and information to make accurate predictions about what will be the solution of this mystery.
Some of you may ask, why is it a mystery at all? Itachi confessed to Naruto, after all? But, in my opinion, much is still unexplained.
Let me try to pose a few old questions again:
How did Itachi kill the entire Uchiha clan, especially without getting wounded himself?
Even Sasuke has doubts about this, and Itachi confirms them. (manga/Naruto/385/4)
In the light of what we know, I think that the only explanation is that Itachi did not do it alone. The question is to what extend he was involved, but IMO, the massacre was done by the entire Root organization.
Itachi's role was just to take the blame for them. That is why Danzo kept saying about Itachi's sacrifice! Itachi did this in order to save Sasuke, and that is also why Sasuke was not harmed by Root.
Also, such an explanation fits another piece of the puzzle: Danzo had a much better motive than Itachi to kill the Uchiha. As a matter of fact, the massacre perfectly fits Danzo's twisted way of thinking. The Uchiha were a threat to Konoha, and he wanted the Sharingan.
In the light of this, Sasuke's determination to destroy Konoha also makes more sense. It is impossible to identify Root members, and many Konoha ninja could have been in Root. So why not to kill them wholesale?
However, another important question remains: what was Madara's role? And here is an intersting new fact: Itachi did not know that Madara knew about his agreement with Danzo!
(manga/Naruto/549/8) Itachi says: "Goddamn you, Madara... So you did know..."
Now what does this tell us? If Itachi was involved in the massacre together with Danzo, then Madara could not have been on their side. Either Itachi was not involved in the massacre at all, or Madara was not on his side!
However, here is another conjecture that I think is important. Let's begin with another question:
Why did the Uchiha rebel?
Of course, we have Madara's explanation about the discrimination of the Uchiha in Konoha. However, look at the facts: the Uchiha were quite well off. They had an important position in Konoha. Why should they have risked it all, if there was not immediate threat? How could they think that their coup would succeed?
One possible answer is that they were manipulated. And, of course, the main candidate for doing this is Madara. This is how he has worked, behind the scenes, by plotting and manipulating people (like the fourth Mizukage or Nagato).
Madara could have persuaded Uchiha leaders that with his support, the coup would be successful. Or, he could even have put some of them under the Tsukuyomi genjutsu (recall that it is stronger than the ordinary Sharingan).
And here we come to another part of the mystery: the role of Uchiha Shisui.
If Madara was behind the plot of the Uchiha, then perhaps Shisui was the one who discovered it. At the time, Shisui was the only Uchiha besides Madara who had the Mangekyo Sharingan. That means that he would be able to see through Madara's genjutsu, and recognize that he was manipulating the Uchiha.
I think that the meetings that the Uchiha have held (manga/Naruto/222/2) concerned their plot, and that during these meeting Shisui discovered Madara's involvement. I think that it was then that Shisui decided to betray his clan to Danzo. It may be that Shisui was in Root. However, Shisui could not bear this and committed suicide.
Still, Shisui wished that Itachi would be capable of confronting Madara after his death. For this, it was necessary for Itachi to have the Mangekyo. This is why he asked Itachi to witness his death.
In order to strengthen Itachi further, Shisui gave him one of his eyes. The other one he gave to Danzo.
An unresolved issue is still why Itachi did not tell the whole story to Naruto and Sasuke. I think it is because the truth would not have persuaded Sasuke to turn aside in his vengeance. Itachi tried to point the entire blame at Madara, instead, during his last conversation with Sasuke.
And Itachi does not want Naruto (and the other Konoha ninja) to know the truth about the role of Root. I am not sure why; but for this reason Itachi decided to take the whole blame himself, and later to blame Madara. Of course, if I am correct, than Madara is still responsible for the massacre, because he persuaded the Uchiha to rebel.
Everyone, please correct me if I am wrong, and tell me what you think. I really believe that we can solve this mystery together!

Some of you may ask, why is it a mystery at all? Itachi confessed to Naruto, after all? But, in my opinion, much is still unexplained.
Let me try to pose a few old questions again:
How did Itachi kill the entire Uchiha clan, especially without getting wounded himself?
Even Sasuke has doubts about this, and Itachi confirms them. (manga/Naruto/385/4)
In the light of what we know, I think that the only explanation is that Itachi did not do it alone. The question is to what extend he was involved, but IMO, the massacre was done by the entire Root organization.
Itachi's role was just to take the blame for them. That is why Danzo kept saying about Itachi's sacrifice! Itachi did this in order to save Sasuke, and that is also why Sasuke was not harmed by Root.
Also, such an explanation fits another piece of the puzzle: Danzo had a much better motive than Itachi to kill the Uchiha. As a matter of fact, the massacre perfectly fits Danzo's twisted way of thinking. The Uchiha were a threat to Konoha, and he wanted the Sharingan.
In the light of this, Sasuke's determination to destroy Konoha also makes more sense. It is impossible to identify Root members, and many Konoha ninja could have been in Root. So why not to kill them wholesale?
However, another important question remains: what was Madara's role? And here is an intersting new fact: Itachi did not know that Madara knew about his agreement with Danzo!
(manga/Naruto/549/8) Itachi says: "Goddamn you, Madara... So you did know..."
Now what does this tell us? If Itachi was involved in the massacre together with Danzo, then Madara could not have been on their side. Either Itachi was not involved in the massacre at all, or Madara was not on his side!
However, here is another conjecture that I think is important. Let's begin with another question:
Why did the Uchiha rebel?
Of course, we have Madara's explanation about the discrimination of the Uchiha in Konoha. However, look at the facts: the Uchiha were quite well off. They had an important position in Konoha. Why should they have risked it all, if there was not immediate threat? How could they think that their coup would succeed?
One possible answer is that they were manipulated. And, of course, the main candidate for doing this is Madara. This is how he has worked, behind the scenes, by plotting and manipulating people (like the fourth Mizukage or Nagato).
Madara could have persuaded Uchiha leaders that with his support, the coup would be successful. Or, he could even have put some of them under the Tsukuyomi genjutsu (recall that it is stronger than the ordinary Sharingan).
And here we come to another part of the mystery: the role of Uchiha Shisui.
If Madara was behind the plot of the Uchiha, then perhaps Shisui was the one who discovered it. At the time, Shisui was the only Uchiha besides Madara who had the Mangekyo Sharingan. That means that he would be able to see through Madara's genjutsu, and recognize that he was manipulating the Uchiha.
I think that the meetings that the Uchiha have held (manga/Naruto/222/2) concerned their plot, and that during these meeting Shisui discovered Madara's involvement. I think that it was then that Shisui decided to betray his clan to Danzo. It may be that Shisui was in Root. However, Shisui could not bear this and committed suicide.
Still, Shisui wished that Itachi would be capable of confronting Madara after his death. For this, it was necessary for Itachi to have the Mangekyo. This is why he asked Itachi to witness his death.
In order to strengthen Itachi further, Shisui gave him one of his eyes. The other one he gave to Danzo.
An unresolved issue is still why Itachi did not tell the whole story to Naruto and Sasuke. I think it is because the truth would not have persuaded Sasuke to turn aside in his vengeance. Itachi tried to point the entire blame at Madara, instead, during his last conversation with Sasuke.
And Itachi does not want Naruto (and the other Konoha ninja) to know the truth about the role of Root. I am not sure why; but for this reason Itachi decided to take the whole blame himself, and later to blame Madara. Of course, if I am correct, than Madara is still responsible for the massacre, because he persuaded the Uchiha to rebel.
Everyone, please correct me if I am wrong, and tell me what you think. I really believe that we can solve this mystery together!