Okay Yuki, that is what I figured too but then why would Itachi being the genius that he is not figure that out. If he figured Madara was still alive and working behind the scenes to cause this war then he had to know that sooner or later Madara would begin stirring things up again like he is doing now. If Itachi had enough power to take out Madara or even just enough to incapacitate him or something why didn't he take care of Madara back then.

The whole reason this thing started as far as was explained was because the Uchihas were being blamed for the Kyuubi attack. Even Sasuke the dope that he is figured that Madara was the one behind the Kyuubi attack so why didn't Itachi just take out Madara as soon as he figured out he was alive and then tell the elders that it was Madara behind the attack and not the Uchihas. Or for that matter why not just tell the Uchihas that it was Madara behind the attack and that he was blackmailing them to cause a war. The Uchiha should have believed him because they already knew that it wasn't them that was responsible for the attack and they would know better than anyone else what Madara is capable of. I mean even Jiraiya with what little information he had came to the conclusion that Madara was responsible so its reasonable to think that people in the village would have had their suspicions too. The very reason they pointed the finger at the Uchiha is because they knew one had attacked the village with the Kyuubi before and now Itachi had proof.

That is of course if Itachi had the power the stop Madara in the first place which I think he did. Even if he didn't all he had to do was inform them of the fact that Madara was there and that alone should have been enough to quell the Uchiha if not stop all hostilities all together because the Third was trying to forge a truce in the first place. They said he killed the clan to prevent war but at best all he did was delay the inevitable.

Then there is the matter of what exactly Minato knew. Jiraiya surmised that Minato figured out Madara was alive and was planning something big which is why Minato did what he did. Now as for what Minato did, why did he do it. If he figured out that Madara was involved with the Kyuubi, whether Madara's power is related to the Kyuubi or whether he was just using the Kyuubi to stir things up. Why didn't Minato just seal all of it away why separate the ying and the yang chakra and seal away the ying and put the yang in Naruto. Unless having the Kyuubi was necessary for something important something that was worth risking Madara getting his hands on it again. This could have something to do with why Madara is using Akatsuki to collect the bijuu in the first place.

Then there is the matter of why the Uchihas needed to be killed. Coup D'etat or not I can't see any reason why all the Uchiha needed to be killed. I'm sure Sasuke wasn't the only one of the Uchihas who was unaware of what was going on so why did they all need to be killed. If it was just to prevent a coup then only the ring leaders would need to be killed possibly the rest of the police force could have been dealt with too or just arrested and imprisoned but why did they all have to die. Why did those like Sasuke who were unaware of everything still needed to be killed and why were those who weren't a threat like Sasuke's aunt and uncle who weren't even ninjas and so couldn't even use the sharingan needed to be killed as well. Why was Danzo so adamant about every Uchiha to a man being killed to the point that after the third died Itachi had to return to the village just to ensure that Sasuke wouldn't be killed.

Putting down political unrest is one thing but this seems more like they were cleansing the village of the Uchihas and I can't think of why that would be necessary. It wasn't because of the threat of the Kyuubi attacking because it was effectively sealed away and even so in that case only those with the sharingan would need to be killed. This seems more like the Senju wanted all the Uchihas killed for some reason and they just used the coup as an excuse to eliminate them.