The opening scene of the movie shows Naruto battling a monster, only to be killed by it. A funeral is held for Naruto in his home village, to which Sakura Haruno, Rock Lee and Neji Hyuuga are shown to attend, along with others. The setting then returns to a few days previous, where a man named Yomi (named after the Japanese word for "underworld") attacks a shrine to retrieve the spirit of Mouryou, a demon who attempted to take over 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 Mouryou's original one.
The only threat to Mouryou's plan is a priestess named Shion, who has the ability to seal his spirit away once more. 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.