The opening scene of the movie showed Naruto fighting a monster, only to be killed by it. The setting then went back to a few days previous, where a man named Yomi (the word meaning the Japanese underworld) attacked a shrine, to retrieve the spirit of Mōryō, a demon who attempted to take over the world and create his "Thousand Year Kingdom". Since he was lacking a body, Yomi offered his as a temporary substitute, until they could retrieve Mōryō's original one.
The only threat to Mōryō's plan was a priestess known as Shion, who could seal his spirit away once more. He raised a stone army from their slumber, to attack the rest of the world, while his four subordinates went to kill Shion. They were given special chakra creatures to enhance their strength.
To deal with the threat, Konohagakure sent out many advance teams to stall the stone army. Naruto Uzumaki, Sakura Haruno, Neji Hyūga and Rock Lee were sent to guard Shion, and deliver her to the shrine where Mōryō's body was kept. They fended off her four would-be assassins, who exhausted themselves in a failed attempt to kill Naruto. Shion told Naruto of his upcoming death; while initially skeptical, her assistant, Taruho, explained that Shion could see the future, and all 100 predictions she had made had come true. As they headed for the shrine, the group was ambushed once again, and split into two teams. Lee killed one of his opponents by eating an alcoholic candy to get him into Drunken Fist, while Naruto was kept busy by his. Neji told Sakura to escape with Shion, unaware that his two opponents were actually just one man and a puppet. Sakura was disabled by the remaining ninja, and Shion was killed.
This turned out to be a ruse: the dead "Shion" was actually Taruho, who transformed himself into a copy of Shion to trick them into thinking they killed the real one. Shion explained that her power worked by allowing her spirit to jump back in time at the moment of her death, thereby allowing her to avoid it by having someone die in her place. Naruto insisted that he would not die, and likewise would keep Shion safe.
Thanks to Lee, Neji realised that the remaining three ninja must keep replenishing their chakra to battle effectively. Naruto was sent on ahead with Shion, while Sakura and Lee tricked their opponents into wasting their chakra on futile attacks. When it came time to replenish their chakra, Neji disabled the final ninja, who was providing it, leaving the other two powerless against Lee and Sakura.
At the mountain temple where Mōryō's body was kept, Naruto and Shion found the stone army waiting. Naruto held the army back while Shion headed inside to begin the sealing ritual. Yomi was already inside, and tricked Shion into beginning the technique with him inside the barrier, allowing Mōryō's spirit to reunite with his body. Naruto came to rescue her. About to see her prediction of his death come true, she used her power to change Naruto's fate, intending to kill herself and Mōryō in order to save him. Naruto stopped her seconds before her death, and used Naruto and Shion's Super Chakra Rasengan, with both their chakra, to destroy Mōryō. With Mōryō gone, Naruto asked Shion what she intended to do now. She replied that Mōryō was a demon caused by the evil thoughts, and that there was bound to be another Mōryō someday. Because of this, she said that she must continue the line of priestesses, that would suppress demons like Mōryō. Then she asked Naruto if he would help (indirectly asking if he will father her child), which an ignorant Naruto happily agreed to.