That Is Why
Spoilers from the manga chapter 451 onwards
(A Conversation between Danzo and Naruto)
"The new Hokage has given permission to dispose of Sasuke as a missing-nin."
These were the words drumming through Naruto's mind as he stormed into Danzo's tent to demand he change his mind about marking Sasuke as a missing-nin and rescinding the kill orders that came with it.
"Danzo, what the hell do you think you are doing marking Sasuke as a missing-nin?" asked Naruto as he entered Danzo's makeshift command center.
"Tell me Uzumaki, what is Uchiha Sasuke to Konoha?" asked Danzo seemingly not bothered by a Genin barging into his office and demanding answers.
"He is one of us, a comrade my teammate. He is a ninja of Konoha." Naruto answered confidently with forceful conviction behind his words, "Which is why you cant mark him as a missing-nin." he told Danzo sounding like he was ordering the Hokage. A tone of voice the battle hardened and experienced political mastermind picked up on and decided to put an end to this.
"I see so he's one of us then tell me is this the same "comrade and teammate" that almost killed you?" asked Danzo in a neutral voice that betrayed nothing, he continued without giving the agitated Naruto a chance to answer, "Is this the same Uchiha Sasuke that betrayed and abandoned Konoha to gain power by going to one of Konoha's most dangerous enemies?"
"He was under the influence of the Curse Seal that Orochimaru gave him. He wouldn't have left if it hadn't been for that." said Naruto desperately trying to make his point so that he could one day save the one he considered his closest friend.
"Our intelligence sources (His Root) has reported that he no longer had the seal after this fight with his brother." said the Rokudaime Hokage "So why did he join Akatsuki after said event, he could have come back to Konoha, like you so passionately pointed out that he was one of us but he choose of his free will to join the most dangerous organization in the Shinobi nations." he finished and waited for Naruto to speak in defense of his long gone friend.
"He wouldn't have just joined then, I know him he wouldn't have he must have been forced somehow or there might be some reason...." and Naruto would have kept going in his unflinching proclamations of the Uchiha's innocence had Danzo not interrupted him.
"Enough!" said Danzo finally raising his voice which had been neutral throughout the meeting, having gotten tired of Naruto's rant "It matters little whether he was forced into it or not he was involved in kidnapping one of Kumo's Jounin the Raikage's brother no less" he said returning to his normal calm voice "If he is not marked as a missing-nin than he remains associated to Konoha as one of its ninja, and since he was wearing Akatsuki clothing during the kidnapping and he was not marked as a missing-nin one could come to the conclusion that Konoha and its ninja are supporting the Akatsuki." he said as he rose from his sitting position to look over the destroyed village of Konoha from his tent window "This would give Kumo a just cause to declare war on Konoha but not just Kumo all the other nations that have been affected by Akatsuki in any way be it death of their ninja or kidnappings of their Jinchuuriki's, look around Uzumaki, Konoha is nowhere ready to handle a full out war with anyone let alone a war with one of the great five villages."
"But.. But... You cant just kill him..." shouted Naruto getting hysterical not believing one bit that his friend could potentially cause Konoha so much damage.
"Oh and what would you have me do, send him a come back soon card? or perhaps risk more of my ninja by sending then to retrieve a traitor during which I might add they would have to hold back as to not kill said traitor whereas he would have no qualms about killing them" said Danzo somewhat amused at the blind faith the orange wearing idiot had in his so called friend.
"No you don't have to send anyone else, just send me give me some time to bring him back." Naruto said pleading to the Hokage hoping he would listen and send him to retrieve Sasuke so no one else had to risk their lives.
"No." commanded Danzo in a voice that left no place for negotiations "You are Konoha's vessel, in our weakened state we cannot afford for you to leave the village to go play house with you friend, you will be staying in the village until further orders."
"You cant do that to me.." said Naruto obviously agitated.
"Yes I can, I am not Tsunade who seems to baby you and lets you off for anything, I am the Hokage of this village and you will obey my orders." said Danzo
"But we have to bring him back... he is one of us, If I were the Hokage I wouldn't just kill one of our own.." shouted Naruto and would have kept at it had Danzo not signaled his guards to knock him out but the last thing he heard before slipping into his forcefully induced sleep was
"And that is why I am the Hokage and you a genin Uzumaki.."
I quite like Danzo as the Hokage, would I have prefered Naruto or Kakashi as the Rokudaime yes but I think Danzo will do some good and get then acting like real ninja and not like some love sick do gooders at least he is not going to overlook things, like marking Sasuke as a missing-nin but I think he did that for his own benefit so that we wouldn't get to the village alive and ruin his chances at the big chair with the vote coming up. Meh first story just something that has been going through my head.