In the potential outbreak of a Fourth Great Ninja World War, a few ninjas with Kekkei Genkai abilities had disappeared from the land of Lightning, Earth, Water and Wind. The Land of Fire remains the only village not affected by these events that people start to suspect its role in these incidents, and rumors of a possible rebellion begin to circulate. With the other nations amassing troops on the borders of the Land of Fire and threatening invasion, the Feudal Lord of the Land of Fire orders Tsunade to capture the real culprit and prove Konoha’s innocence, in the event of failure and the Land of Fire decides to destroy the village to preserve world peace.
Hiruko is a missing-nin culprit and former friend of the Legendary Sannin (Orochimaru, Jiraiya and Tsunade), who left Konoha long ago after developing the Chimera Technique, a jutsu that allows the user to absorb both the chakra and Kekkei Genkai of other ninja. Based in Mount Shami with his followers, Ichi, Ni and San, Hiruko uses a jutsu to project himself onto the skies above Konoha, announcing that he will obtain the Kekkei Genkai of the Land of Fire and become immortal and invincible, instigating the Fourth Great Ninja World War and conquer the world. With Hiruko intending to use the power of a solar eclipse to carry out his plan, a race to defeat him begins as the moment of the eclipse draws near.
Hiruko targets the Land of Fire’s Kekkei Genkai, Kakashi’s Sharingan. One night, Hiruko activates a Puppet Curse placed on Kakashi over ten years ago. Kakashi asks Tsunade to allow him to go, so he can defeat Hiruko. Before he leaves, Kakashi asks Tsunade to place a special seal on him that will automatically activate Kamui, when Hiruko attempts to absorb him. Under the influence of Hiruko’s Puppet Curse, Kakashi leaves the village. At the Hokage’s office, Tsunade labels Kakashi as a missing-nin and orders everyone from the village without any further orders from her to stay away from Kakashi. Upon hearing of his desertion, Naruto and Sakura leave the village to pursue and rescue their teacher. Team 8, Team 10 and Team Guy are sent to retrieve them.
Naruto, Sakura and Sai follow Kakashi, and defeat Hiruko’s subordinates. Eventually they reach the temple, where Hiruko awaits for Kakashi. Naruto enters the temple alone, where Hiruko starts the eclipse and the absorption. However, Kakashi’s Mangekyō Sharingan activates, and the space inside the slime created by the Chimera Technique begins to distort. Naruto saves Kakashi, breaking into the slime with multiple Rasengans and pulls him out, but Hiruko remains alive. He states that the eclipse continues and releases a large amount of chakra, reducing the surrounding area to rubble. Hiruko summons a chimera beast. Team 8, Team 10 and Team Guy work together and defeat the chimera beast. Naruto and Kakashi battle Hiruko who easily absorbs their attacks, Raikiri and Ōdoma Rasengan. Naruto finally attacks Hiruko with Fūton: Rasenshuriken (Wind Release (Wind Style): Rasenshuriken), that Hiruko fails to absorb it and dies from his injuries. The Konoha ninja celebrate their victory at Mount Shumi.
After the credits, a note from Masashi Kishimoto says, “I hope this movie stays with you forever…”