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Amegakure (雨隠れの里, Amegakure no Sato; Literally meaning "Village Hidden by Rain") is a small, yet highly industrialised hidden village located in an unnamed country. Its architecture is composed of several metallic skyscrapers with rowed ducts connected to them and many power lines surrounding. As its name suggests, it rains almost constantly due to a storm above the village. All the water seemingly ends in a large lake that surrounds the village. A number of smaller villages also surround Amegakure.
There are many ninja from this village who are skilled genjutsu users. It is a hidden village that one by one raises the ability of its shinobi, in turn working out original techniques. They also developed assassination techniques, getting numerous requests from foreign countries because of this.
For many years, Amegakure was led by Hanzō; he led Amegakure's forces against Konohagakure during the Second Shinobi World War. Despite the fact that Hanzō had a huge presence on the battlefield, such that he slaughtered an entire Konoha platoon and allowed ninja as powerful as the young Sannin to live when they managed to hold their own against him, Amegakure lost the war. Amegakure's location between three of the Five Great Shinobi Countries has caused it to serve as a battleground during the various ninja wars, making most of its population war refugees. Amegakure has adopted a heavy isolationist policy because of this, leading to the village's defences to be abnormally impenetrable. To be admitted to the village, visitors, even those coming for Chūnin Exams held in Amegakure, must go through a number of security checks and are under constant surveillance during their stay. Even Hanzō, despite his strength was paranoid and constantly feared being assassinated and as such was rarely seen in public.
During the Third Shinobi World War, a group from Amegakure began advocating peace. When their group became large and popular enough, Hanzō saw this as a threat to his rule. He allied with Danzō Shimura of Konohagakure to have the Akatsuki eliminated. Hanzō lured them to an ambush by claiming to be interested in their ideas and Yahiko, the group's public leader was killed. Nagato tried to take revenge on Hanzō, but succeeded only in killing the other Amegakure ninja present as well as all of Danzō's Root personnel as Hanzō escaped the slaughter.
Nagato, adopting the alias of Pain, soon began a civil war within Amegakure. Forces loyal to his new ideas for the village wore an Amegakure headband with a horizontal slash through the middle, showing their rejection of the former Amegakure leadership and principles. Pain eventually single-handedly killed Hanzō as well as everyone even remotely affiliated with him. He similarly slaughters any remnants loyal to Hanzō that tried to sneak back into the village to assassinate him. Pain's effectiveness has caused the villagers of Amegakure to regard him as a god. The people of Amegakure began to refer to Pain as "Lord Pain", and to Konan who assisted Pain, as "Lady Angel".
During Nagato's reign, he used a technique that made it rain every Sunday or whenever he had to leave the village. The special rain was connected to his senses, and allowed him to sense intruders who tried to enter the village, making infiltration impossible without being detected. After Nagato's death, Konan assumes the duties of Amegakure's leader and swears the village's allegiance to Naruto Uzumaki, but she falls in battle against Tobi, who came to retrieve Nagato's Rinnegan.
Knowledge of Amegakure's civil war was not common throughout the ninja world, and the fate of Hanzō himself was completely unknown to the point that other villages believed him to still be in charge. Because Pain uses the village as his base of operations for Akatsuki, Jiraiya was able to spread news of these developments during the course of his investigation into the organisation. Pain later went to Konohagakure to try to capture Naruto and the Nine-Tailed Demon Fox respectively, after killing Jiraiya. He effectively destroys the majority of Konoha's infrastructure and kills many of its citizens. Later, he is convinced by Naruto's determination and ideals so he decides to revive those who he recently killed using the Outer Path: Samsara of Heavenly Life Technique. In this village it rains almost constantly except for when Pain would stop the rain. The only natural incidence of the rain ending was during Konan's fight with Tobi who had come to retrieve the Rinnegan. After Konan's death, however, it is unknown who leads the village.
- Twenty-one genin from Amegakure participated in the Chūnin Exams, far more than the other minor villages.
- Many characters from Amegakure, such as Shigure and Aoi Rokushō, have been seen using umbrellas that have hidden weapon mechanisms in them. Also, many shinobi from this village wear simple rebreathers.