The film concerns the potential outbreak of a Fourth Great Shinobi World War when ninja with Kekkei Genkai abilities begins to disappear from Kumogakure, Iwagakure, Kirigakure, and Sunagakure. The other nations suspect Konohagakure – the only village left unscathed – of causing the incident, and rumors circulate that they plan to rebel. With the other nations amassing troops at the Land of Fire’s borders, threatening invasion, the lord tries to find those responsible and prove Konoha’s innocence; in the event of failure, the Land of Fire will be forced to destroy the village in order to preserve world peace.

The true culprit and main antagonist of the film, Hiruko, is a missing-nin and former friend of the Sannin (Orochimaru) who disappeared from Konohagakure dozens of years earlier, after developing Chimera Technique, a jutsu which allows him to absorb both the chakra and Kekkei Genkai of other ninja. Based in Mount Shami with followers, Ichi, Ni, and San, Hiruko uses a genjutsu to project himself in the skies above Konoha, announcing that he will obtain the Kekkei Genkai of the Land of Fire and become immortal and invincible, then instigate the Fourth Great Shinobi World War and conquer the world. With Hiruko wanting the last of the Kekkei Genkai, he eventually becomes interested with Kakashi, due to the fact he has the Sharingan. Hiruko plans to get the Sharingan no matter what, even going as far as to controlling him to do his bidding. With Hiruko intending to use the power of the solar eclipse to carry out this plan, a race to defeat him begins as the moment of the eclipse draws near.

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