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During Pain's assault on the Leaf, Danzo and the Elders didn't want Pain to get the Nine Tails to protect the village from destruction. But, hiding what Pain wants makes him destroy the village! That is to say, Pain was looking for Naruto/the Nine Tails, but Danzo didn't want to recall him and killed the toad messenger. But, by denying Pain what he wanted, he allowed him to really destroy the village.

Why did Danzo do that?

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  • Danzo couldn't have known that Naruto returning to the battle would help turn the tide in the battle against Pain.

    After all, on the one hand almost nothing is known about the mysterious leader of the Akatsuki. What is known is that Pain is so powerful that he even managed to kill Jiraiya, one of the legendary Sannin.

    On the other hand, Naruto is (to the best of everyone else's knowledge) not yet of the caliber of Jiraiya. Naturally, Danzo (and others) cannot have known that Naruto had already surpassed his master by becoming a perfect sage. So, he couldn't have concluded that recalling Naruto would help win the battle against Pain and thereby prevent the destruction of the village.

  • Danzo is also gambling on Pain's attack being so devastating that Tsunade's term as the Hokage will come to an end because of it, either because she becomes incapacitated (or worse), or because of the immense loss in trust in her leadership due to the losses sustained from Pain's attack. In fact, he specifically instructs his ANBU to remain hidden instead of facing Pain head on, so that once the chaos overhead clears, Danzo can (almost literally) emerge from the shadows to become the new leader of Konohagakure.

    So, preventing the destruction of the village is not very high up on Danzo's list of priorities. Quite the opposite, in fact.

  • Lastly, recall that Danzo views Naruto as nothing more than a weapon, a military asset for the village. He does not separate Naruto from the Kyuubi that he is hosting (indeed, most jinchuuriki have been viewed in the same manner throughout the history of the show). Thus, if Naruto is recalled back to the village then there is a high possibility that the Kyuubi will fall into the hands of the Akatsuki. That would be a huge blow to Konoha's military might, and Danzo wants to avoid this situation at all costs.

    (Compare this with Tsunade's perspective. When she berates the two village elders, she tells them about how Naruto should be viewed as a Konoha shinobi, and that it is high time they learn to rely on him as a comrade instead.)

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Danzo did not have any control over Naruto while he was on Mount Myobuku. Danzo did not have an affinity for frogs and he really had no way to contact Naruto. Also Naruto was doing important training there that he had to finish before returning to Konoha. Danzo probably did not want to rush Naruto's training and risk him not completing it.

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    Considering that he killed a frog to prevent them from contacting Naruto I don't think lack of communication was the issue.
    – Joe W
    Sep 22 at 16:57

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