I did my AP Lit Final project on Naruto. If you think about it for a little while this will make sense. The story behind the development of Nagato is a political allegory regarding terrorism. When Tendo Pain is talking to Naruto during their battle, he mentions the 3 superpower nations using the hidden rain as a battleground. The hidden rain being neutral in the war was repeatedly destroyed and destabilized when the great nations battled. Once the war was over, the hidden rain was left in a very unstable state while the great nations profited.

Later, after the akatsuki is formed, danzo of the leaf incepts hanzo the salamander too believe the akatsuki is a threat to his rule. Thus when the akatsuki meet with hanzo and danzo, Nagato is forced to kill yahiko.

During the battle when Tendo Pain pins Naruto down and talks to him, Nagato tells the story of how the lead did what he had just done to the leaf before Naruto was born. Naruto begins to understand some of pains motivation and is unable to immediately answer pains question about how he would go about world peace- end the cycle of hatred.

Later in the series you learn more about danzos influence in the leafs involvement with internal and external conflicts, sasuke (uchiha clan) and Nagato (hidden rain)

Danzos constant battle with hiruzen sarutobis teachings and how they go about foreign policy.

Tsunade tells how danzo makes his decisions based on logic, and it is obvious danzo only acts with the intent of supporting the leaf. This can be viewed as Conservative thought. A “leaf first” policy if you will. Hiruzen sarutobis teachings were based around diplomacy and how danzos actions woukd have a long term effect on the leaf. Sarutobis teachings can be viewed as liberal or progressive thought.

Danzo always acted with the intent to support the leaf, but without considering ling term side effects, it ended up causing much more severe problems for the leaf in the years to come. This is paralleled to the US involvement in Iraq, and how the wars there destabilized the middle East (hidden rain) and now terrorist groups such as al queaeda and ISIS (akatsuki) have formed.

The more you think about it the more consistant it gets. Very interesting stuff. Writers of Naruto were feeling the Bern