A mysterious group of ninja called the Sora from the Sky Country makes a surprise attack on the Leaf for vengeance, due to them nearly destroying the Sky Country, during the Second Great Shinobi World War. At the same time, Naruto, Sakura and Hinata are sent along to help a boy’s village. They accompany Akamaru and Doctor Shinnō back to the village. Later, Naruto learns that Amaru is really a girl, due to her falling into the water for her scapel.
Meanwhile, at Konoha, the Sora-nin retreat with their dwindling chakra supply. Tsunade sends another special team, consisting of Kakashi, Shikamaru, Sai and Shino to look for their base. Later, Sai and Shino successfully destroy the ships which the sky ninja are stationed and thus leaving Konoha victorious.
At Orochimaru’s lair, Orochimaru is now ill, due to body transfer jutsu, he used is nearly expired. He orders Sasuke to get a man, who is able to help him perfect his reincarnation jutsu. Naruto and company reach Amaru’s burning village, where Amaru triggers a trap while searching for all of her villagers, but Shinnō protects her and dies in the process. After Amaru comes to her senses, they continue to look for villagers.
Later, Hinata is separated from the team. Naruto and Sakura later find themselves in front of an evil monster called Reibi the Zero-Tails, a being that feeds on the darkness of human souls and had somehow possessed Amaru. After knocking Sakura unconscious, Reibi senses that Naruto has a huge dark energy inside of him, so it taunts Naruto and makes him using the power causing him to take on the Nine-Tailed Fox chakra, and eventually goes into four-tails state. The present Sakura gave Naruto from Jiraiya contained a seal, which suppressed the Nine-Tailed Fox chakra, allowing Naruto to take over. Naruto tells Amaru to ignore the darkness in her heart to destroy Reibi. While Sakura returns to the village for help, Naruto and Amaru enter the ruins that rises up from the ground to reveal Ancor Vantian, a floating fortress, where they successfully find Shinnō alive.
Amaru happily hugs him that he is alive, but Naruto notices something is wrong with Shinnō who betrays Amaru for trusting him, breaking her heart. Shinnō mentions that he uses Amaru the whole time, researching the power of darkness for about fifteen years and he finally found it in Konoha, a secret scroll. He then transforms into a powered-up form allowing him to even access the eight gates, and attacks to fatally wound Naruto with his Revival technique. Amaru desperately tries to commit suicide with a blade, but Naruto stops her, getting stabbed instead. Amaru reminisces about her past, that when she was small, she suffered from a strange illness. No one helped her, fearing that they would be infected. However, Shinnō cares about and cures her. She admits her love to Shinnō, but he evilly laughs at her, distracting him. So, Naruto heroically attacks Shinnō. Before finishing him off with the Rasengan, Sasuke appears and intervenes Naruto’s attack with Chidori Senbon. Sasuke tells the weakened Shinnō (who loses his muscular power a few minutes earlier) that Orochimaru needs help, but after giving the reincarnation jutsu scroll to Sasuke, Shinnō refuses to cooperate and falls into the trap door. Naruto and Sasuke end up in a room with a giant cocoon, that absorbs dark chakra. Shinnō reveals the cocoon to be the Zero-Tails, fusing himself along with it and transforms into a monster, that captures them and starts to absorb their chakra. After Sasuke releases his curse seal and Naruto with his Nine Tailed Fox chakra to break free from Shinnō’s grasp, they overload him and defeat him with a Chidori and Tornado Rasengan respectively. Shinnō reveals now that Reibi is unleashed, whose energy starts to overtake the fortress. In the meantime, Konoha successfully infiltrates and destroys the Sora-ninja’s base. Amaru finds the villagers and Hinata in a cell and frees them all. Naruto re-appears and orders Amaru to leave the ruins, while he remains there to destroy it. Believing that he helps Naruto who smiles and says a silent goodbye, Sasuke leaves. Encouraged by Jiraiya, Naruto destroys the fortress with the Determination Rasengan and falls through the sky. So, Amaru grabs the Sora glider that she drops and successfully saves him. They landed safely on Gamabunta, summoned by Jiraiya.
After returning and giving the scroll to Orochimaru, Sasuke later thinks of Naruto’s goodbye and uses the Chidori at the pond.