A mysterious group of ninja from the land of sky makes a surprise attack on the Hidden Leaf Village for vengeance due to the Leaf Village nearly destroying the Sky Country during the last Shinobi World War. At the same time Naruto, Hinata, Sakura and Team Sonic are sent along to help a boy's village. They accompany Amaru, the boy, and his sensei, Shinnou, back to the village. Everyone then finds out Amaru's a girl due to her falling into a river for her scapel.
Meanwhile at Konoha, the sky ninja retreat with their dwindling chakra supply. Lady Tsunade sends another Team consisting of Kakashi, Shikamaru, Sai, Shinno, Espio, Jet, Rayman, and Silver to look for their base. Later on, as the movie progresses Sai, Shinno, Jet, and Silver successfully destroy the ships in which the sky ninja are stationed.
At Orochimaru's lair, Orochimaru is ill because the body transfer jutsu he uses is close to expiration. He orders Sasuke Uchiha to get a man who is able to help him perfect his reincarnation jutsu. Naruto and Team Sonic reach Amaru's village and finds the village completely destroyed. Amaru triggers a trap while searching for any survivors but her sensei protects her and dies in the process. After Amaru comes to her senses they comtinue to look for villagers.
Later on Hinata becomes separated from Naruto, Sakura and Team Sonic. The gang finds themselves in front of an evil monster called Zero Tails, a beast that feeds on the darkness of human souls and somehow possessed Amaru. Sakura proves to be no match for the monster; the creature senses that Naruto has a huge dark power inside of him so it taunts Naruto and tries to mkae him use that power causing him to take on the Nine Tailed Fox chakra and, eventually, goes into four-tails stage. In the beginning, Sakura gave Naruto a present from Jiraiya that contained a seal, suppressing the Nine Tailed Fox chakra, allowing Naruto to take over. Naruto then tells Amaru to forget the darkness in her heart which results in the beast getting defeated.
The gang then decides to seperate; Naruto and Team Sonic continue to look for more villagers and Hinata while Sakura returns to the Leaf Village for more help. Amaru was suppossed to go with Sakura, but stays with Naruto and Team Sonic instead. Immediately, the ruins rise from the ground and reveal Ancor Vantian, a floating fortress. The team decides to search in some parts of the ruins and eventually find Amaru's Master Shinnou alive. Amaru, excited that her sensei is alive runs to hug him, but Naruto and Sonic notices something is wrong and Shinnou laughs at Amaru for trusting him. Shinnou mentions that he has been researching the power of darkness for about 13 years and he's finally found it in Konoha, a secret scroll. He then transforms into a powered-up form and fights Naruto and Team Sonic, overwhelming them with his Revival technique. Amaru reminisces about her past. When she was little, she suffered from an illness. No one tried to help her because they were afraid they would be infected. Only her sensei cared for her and managed to cure her. She admits her love to Shinnou which disracts him, allowing Naruto and Team Sonic to land an attack. Naruto prepares to finish Shinnou off with his Rasengan, but Saskue appears and intervenes Naruto's attack with his Chidori. Sasuke tells Shinnou that Orochimaru with the reincarnation jutsu. At first Shinnou refuses to cooperate and tries to defeat Sasuke until all his power and muscle drain away. Sasuke reveals that he attacked Shinnou minutes earlier with Chidori Senbon at his vital chakra points to cut off his chakra. Shinnou gives Sasuke the scroll to perfect the reincarnation jutsu and leaves via a trap door.
Sasuke leaves and is pursued by Naruto and Team Sonic. They end up in a room with a giant cacoon that is absorbing dark chakra. Shinnou then reveals that the cacoon is Zero Tails, the same monster Naruto and Team Sonic fought. He then fuses in with the cacoon and transforms into a monster. Shinnou captures Naruto, Sasuke, and Sonic and starts absorbing their chakra; Sasuke then releases the curse seal, Naruto releases the Nine Tailed Fox chakra and Sonic turns into his super form, overloading him and freeing them from his grasp and defeat him. Shinnou reveals that Reibi is now unleashed, whose energy starts to overtake the fortress.
In the meantime Konoha successfully infiltrates and destroy's the sky ninja base. Amaru finds the villagers and Hinata in a cell and frees them all. Naruto and Team Sonic appear again, Naruto and Sonic order Amaru and the rest of the Team to leave while they remain and destroy the ruins. Amaru and Phineas refuse but are forced to leave by Sasuke and Shadow. Naruto thanks Sasuke before using Rasengan to send Sasuke away, Naruto also says a silent goodbye. Naruto and Sonic proceed to destroy the ruins sending them in a freefall. Amaru, Phineas, Ferb and Tails see Naruto and Sonic from a distance, Amaru grabs a pair of sky ninja wings and they try to save them. They finally reach them, Amaru grabs Naruto and Tails, carrying Phineas and Ferb grab Sonic. Sonic however can not Grab Amaru and Naruto in time, so they fall together. Tails, Phineas, Ferb, and Sonic are able to land safely. Jiraiya suddenly appears out with Gamabunta and catches Naruto and Amaru, saving them. Sasuke returns and gives Orochimaru the scroll. The Movie ends with Sasuke thinking of Naruto's goodbye to him: "I promise, I' am gonna bring you back to the Leaf".