The film opens with a prediction that Naruto Uzumaki dies battling a monster who kills him. A funeral is held for Naruto at his home village, where others attend. Tsunade looks out at the window and ponders if everything is just decided by fate. The film's scene returns to a few days previous, where a man named Yomi attacks a shrine to retrieve the spirit of Mōryō, a demon attempting to conquer the world and create his "Thousand Year Kingdom". Since he is lacking a body, Yomi offers his as a temporary substitute until they can retrieve Mōryō's original one. The only threat to Mōryō's plan is a priestess named Shion, who has the ability to seal his spirit away once more; she can also foresee a person's death. He raises a stone army from their slumber to attack the rest of the world while his four subordinates go to eliminate Shion. They are given special chakra creatures to enhance their strength. To deal with the threat, the Land of Fire sends out many advance teams to stall the stone army. Naruto, Sakura Haruno, Rock Lee and Neji Hyuga are sent to guard Shion, and deliver her to the shrine where Mōryō's body is kept. They fend off Shion's four would-be assassins, and afterwards Shion prophesies Naruto's upcoming death. Shion's total acceptance of "fate", as well as her selfish attitude, provokes Naruto into antagonizing her. As they head for the shrine, they are again ambushed by the assassins and Shion is seemingly killed. It turns out to be a ruse: the dead "Shion" is actually her servant, Taruho, acting as a decoy by the use of the Shadow Mirror Body Transfer Jutsu. After Neji tells Naruto to escort Shion to the temple alone, Shion explains that her predictions work by using others' lives to protect her own. Naruto insists that he will survive and likewise will keep Shion safe. Together, Sakura, Lee and Neji defeat the assassins, and at the mountain temple where Mōryō's body is kept, Naruto and Shion find the stone army waiting. Naruto holds the army back, while Shion heads inside to begin the sealing ritual, where Yomi tricks Shion into beginning the technique with him inside the barrier, allowing Mōryō's spirit to reunite with his body. After Kakashi Hatake, Might Guy, Shikamaru Nara and Temari destroy the stone army, Naruto comes to rescue Shion. About to see her prediction of his death come true, Shion uses her bell's power to change Naruto's fate. She is able to tap into her true powers, intending to kill herself and Mōryō to save Naruto. Naruto stops her seconds before her death, and creates a giant Rasengan by combining Shion's chakra with his. Naruto drives the Rasengan into Mōryō and obliterates it. In the final scene, Naruto asks Shion what she intends to do now. She replies that Mōryō was a demon created by the dark thoughts of mankind, and that there is bound to be another Mōryō someday. Because of this, she says that she must continue the line of priestesses that will suppress demons like Mōryō. Shion then asks Naruto if he will help her, much to the shock of Sakura, Kakashi and Lee. Naruto, clueless as usual, agrees without realizing the second meaning of her question.
In its opening weekendNaruto Shippuden: The Movie came in at number six. In its second week the movie dropped to number eight and stayed there in its third week.
