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The Second Shinobi World War (第二次忍界大戦, Dainiji Ninkai Taisen) was the second of four great wars involving the majority of the shinobi villages and countries. Not much is known about the politics of this era, but there were known conflicts between Konohagakure, led by the Third Hokage, Sunagakure, likely led by the Third Kazekage, Amegakure, led by Hanzō of the Salamander, and Iwagakure, presumably led by the Third Tsuchikage. The majority of the fighting seems to have taken place in minor countries like Amegakure, leaving them devastated. The eventual outcome of the war seems to have been in favour of Konoha. Nagato referred to it as a war Konoha started.
The First Shinobi World War ended with an armistice treaty, but also left the Five Great Shinobi Countries seriously wounded. The treaty led to a period of peace, but after about twenty years, the economic disparity between the countries had become a serious problem. The nations began to form factions, and under the pretext of expending fair rights, the countries started using military force to expand their territories. Thus, a world war started.
As with all wars, the Second Shinobi World War brought forth many heroes and took even more lives. It was during this war that the legendary "Sannin" (伝説の三忍, Densetsu no Sannin, Literally meaning: Legendary Three Ninja) rose to fame and received their nickname from Hanzō during a skirmish with Amegakure. Tsunade in particular became famous as the world's greatest medical-nin while successfully countering all of Chiyo's poisons. Her ideas and skills revolutionised shinobi squads to include medical-nin she trained personally, increasing mission success and survival rates, a system that remains in place in the present. She is thus cited as having made great contributions to Konoha's victory as well as the current system of all medical-nin. It is also likely that this war was where Sakumo Hatake made his name as "Konoha's White Fang" (木ノ葉の白い牙, Konoha no Shiroi Kiba).
On the other side, it was the war where Tsunade lost her younger brother, Nawaki and her lover, Dan Katō, leaving her with an extreme case of hæmophobia. It was also during this war that Sasori's parents died, an event that eventually made him leave his village and join the Akatsuki later. At the same time, Chiyo swore vengeance against Sakumo for killing Sasori's parents. It is also likely that it was during this war that Sakumo Hatake would fail a mission vital to Konoha's war effort. Subsequentially, he was ostracised and ultimately committed suicide: an action that would shape his son's character for years. The Ame Orphans lost their parents during this war, leading Jiraiya to take care of them for a while, claiming it was the least he could do. One of the orphans, Nagato, would come to desire an end to war because of his experiences from this war, a purpose he used Akatsuki for.
- In the anime, the Sannin's actions during this war are incorrectly stated to have occurred during the Third Shinobi World War. A later episode corrected this error.
- During the war, the Land of the Sky emerged to challenge the Five Great Shinobi Countries, only to be destroyed.