A mysterious group of ninja called the Sora from the Sky Country makes a surprise attack on Konoha. This is because Konoha nearly destroyed the Sky Country during the last Shinobi World War. However, they survived and now are after Konoha and the Fire Country for revenge.
The group starts attacking Konoha, causing mass mayhem, with flying ninjas on winged-mechanical devices bombarding the village. Naruto then appears to help with the battle, until meeting and helping an elder man with a fallen villager. He learns this man is a talented doctor and comes from a neighboring village. The doctor tells him to take the fallen villager to the hospital- then disappears.
At the hospital Hinata and Sakura are both trying to heal the wounded. They begin to talk about how many of the villagers' wounds were previously taken care of before arriving. A boy crashes through the door, looking for his sensei, who is currently in Konoha, that was with him to heal the injured at this village. Naruto comments that he had met the boy's teacher but before he and the boy could talk, he faints in Naruto's arms. Later, Naruto and the old doctor sit beside the boy, named Amaru, and Naruto learns a little of the boy's past.
A 3 man team consisting of Naruto, Sakura and Hinata are sent along to help the boy's village and they accompany Amaru, and Shinno, his sensei, back to the village. The team travel through a forest full of eerie beasts and poisonous animals by small rowing boats down a river to avoid danger. A Sora-Nin suddenly appears, flying over, scoping the area and the group tries to tactfully hide by the riverside. Sakura, Shinno and Hinata glide their boat under overhead trees while Naruto flips his and Amaru's boat- hiding underwater until the Sora-Nin goes. Naruto resurfaces with only Amaru's overcoat in hand. Amaru had dropped his precious scalpel (a gift from his beloved sensei) and accidentally gets caught in the weeds underwater while retrieving it. Naruto dives down into the river then hauls Amaru's body into the boat. While helping Amaru, Naruto notices that Amaru is in fact a "she" due to his feminine figure. Naruto blushes while at the same time, a poisonous piranha-like fish bites him, making him faint. Naruto wakes up a few moments later with Amaru removing the poison from him. Naruto questions Amaru alone and discovers that Amaru is indeed a girl.
Meanwhile at Konoha, the Sora-nin retreat with their dwindling chakra supply (which they need to remain flying). Tsunade sends another special team- Consisting of Kakashi, Shikamaru, Sai and Shino- to look for their base. With a skillful plan by Shikamaru, Sai approaches the ships (which is near the beach) on one of his ink birds to attract attention while Shikamaru and Kakashi hide near the shore waiting for the right time to infiltrate and attack.
At Orochimaru's lair, Orochimaru is now ill because the body transfer jutsu he uses is close to expiration. Kabuto is attending to him and tells Sasuke that the Sora-nin are attacking Konoha to which Sasuke gives an "I don't care" reply. Orochimaru orders Sasuke to get a man who is able to help him perfect his reincarnation jutsu.
Naruto's team finally come into view of Amaru's Village, only to see the tops of all the buildings on fire, smoke billowing overhead. Amaru, in a panic, runs ahead of the team into the closest village gate alone. She cries and runs up a flight of outdoor stairs, trying to find the villagers that had mysteriously all disappeared. She unknowingly triggers a trap that sends hundreds of kunai flying towards her. Saving her, her sensei Shinno steps in and tries to protect her- costing him his life. Naruto, Sakura and Hinata run to the scene but it was too late, Shinno dies because of his wounds. They quickly bury him near the village and the ninja leave Amaru to sulk while they search the near area for the missing villagers.
The three man team splits up. Sakura searches near a misty swamp and runs into Naruto. He points out some large empty ruins in the distance ad they go explore. Naruto and Sakura quietly walk amongst the ruins until they run into Amaru. But this is not Amaru as they know it- they find themselves in front of an evil monster that claims to be a Tailed Beast, the Zero Tails, who feeds on the darkness of human souls and somehow took over Amaru. Sakura proves to be no match for the beast and is knocked unconscious. The creature senses that Naruto has a huge dark energy/power inside of him so it taunts Naruto and tries to make him use that power, saying "He cannot save anyone without it" this makes Naruto remember about his failure in saving Sasuke and is emotionally unstable taking on the Nine-Tailed Demon Fox form, eventually the four tails state. After fighting for a while, he turns back to normal when the seal which Jiraiya gave to Naruto activates and removes Nine Tail's chakra.
Naruto tells Amaru to ignore the darkness in her heart which finally resulted in the beast dissipating. Sakura wakes up in Naruto's arms and punches him - awkwardly. They decided to separate with Naruto going on to look for the villagers with Amaru and Hinata and Sakura going back to get help. Naruto and Amaru run inside a near ruin temple and feel the floor begin to shake. The whole ruin temple, and surrounding ruins emerged from the ground- and began to fly just as the Sora-nin planes. The two find Shinno inside - safe and sound saying something about conquering the world with the power of darkness. Amaru, excited that her sensei is alive runs to hug him, Naruto notices something's not right and Shinno laughs at Amaru for trusting him. Shinno tells that he's been researching on the power of darkness for about 15 years, only using Amaru for her heart of darkness, and he's finally collected enough power to destroy all the ninja villages. He then uses this power to transform into a much stronger version of himself. Naruto charges towards him only to be outmatched again and again, beating Naruto badly.
Fighting, Shinno tries to convince Naruto to use the Nine-Tailed Demon Fox's chakra. A emotionally stunned Amaru cries while Shinno and Naruto yell and destroy each other. She begins to think back on her past. When she was small, she suffered from a strange illness. No one tried to help her, fearing that they would be infected. Only Shinno cared for her and managed to cure her. Naruto tells her not to throw her feelings away while the evil Shinno mocks her. He tells her to finally admit her love and feelings to Shinno, causing him to laugh and allowing Naruto to land a hit. Naruto then manages to gain the upper hand in the fight. He was about to finish him off with Rasengan when Sasuke appears and intervenes Naruto's Rasengan with a blast of Chidori. Saskue then explains how Orochimaru needed the knowledge of the man to help with a reincarnation jutsu to Shinno and in return Shinno gives him a scroll. At first Shinno refuses to do anything and tries to defeat Sasuke with dark chakra until he collapses and all his power and muscle drain away suddenly. Sasuke reveals that he had attacked Shinno minutes earlier with Chidori Senbon at his vital chakra points to cut off his chakra flow. Shinno then flees the scene with Sasuke following after him. Naruto tells Amaru to go find the villagers while he goes after Sasuke. He chases after Sasuke through hallways and asks him what he was doing there and how long he had been. They stop in a large, blue-glowing room, in which is a gigantic cocoon that is absorbing dark chakra. Shinno fuses with the cocoon (that happens to be the fetal form of the Tailed Beast, zero-tails) and attacks Naruto and Sasuke with hundreds of tentacle arms and captures them. Shinno tries to absorb their chakra for his own power. With a plan, Sasuke turns to Curse Seal level 1 and releases evil chakra. Naruto catches on to Sasuke's plan and releases a tremendous amount of his Nine-Tailed Demon Fox chakra. The Tailed Beast can not handle so much chakra at once, and the two break free. Naruto then makes a Nine Tail's chakra-infused Rasengan (called the tornado Rasengan) and attacks. The cocoon creature puts up a shield which Naruto and him reach a stalemate. To aid, Sasuke ascends to Curse Seal Level 2 and cuts down the shield thus allowing Naruto to finish off the creature with Rasengan. After that he and Sasuke escape.
In the meantime, Konoha successfully destroys the Sora-nin's boat base (that Sai was fighting) with Shino's insects. Amaru finds Hinata and the villagers in a cell in the flying ruins and frees them all. They all board a flying lifeboat. Amaru scrambles to reach a launching lever, away from the boat but Naruto appears again and orders Amaru to get in the boat- he would take care of the launch. She refuses and Sasuke throws her in by force. As the lifeboat leaves a tentacle appears and tries to grab it but Sasuke cuts it down. Naruto smiles, and also forces Sasuke off the flying fortress with a Rasengan. Naruto says something to Sasuke, but he's too far off in the distance to hear. Naruto remembers what Jiraiya once said to him, that he had the willpower to never give up, he creates hundreds of shadow clones that all start to destroy the ruins with a Rasengan called "Determination". He collapses and falls from the sky after destroying the ruins. Amaru, from a distance, sees Naruto and grabs a pair of Sora-nin wings and goes towards him. Upon reaching him, she hugs him in midair, and they fall together. As they fall Amaru tells Naruto how she will never let him be alone. The next scene shows Gamabunta, summoned by Jiraiya, inflating his stomach to catch the falling Naruto and Amaru.
Later on, Naruto wakes up in Amaru's arms. Sasuke goes back and gives Orochimaru the scroll, who then asks if something good had happened. Sasuke then goes off to train and thinks of what Naruto said, "I'll definitely bring you back to Konoha, Sasuke!"
[DB] Naruto Shippuuden Movie 2 [1A36E311].avi