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The movie opens with a battle taking place at night on a desolate seaside beach between Sand Ninja and mysterious warriors wearing bulky suits of armor. Despite their best efforts, the Sand Ninja are slowly overwhelmed by the sheer strength of their mysterious opponents.

A mysterious group of ninja called the Sora from the Sky Country makes a surprise attack on Konoha for vengeance due to Konoha nearly destroying the Sky Country during the last Shinobi World War. At the same time Naruto, Sakura, and Hinata are sent along to help a boy's village.

Yamato, Naruto Uzumaki, Sakura Haruno, and Sai are assigned on a mission to capture Mukade, a missing-nin. They all have chakra-knives, which are uniquely-designed trench knives that allow a ninja to infuse their chakra with it to produce an added effect.