Naruto tells Amaru to ignore the darkness in her heart which finally resulted in the beast getting defeated. Sakura wakes up in Naruto's arms and punches him - awkwardly. They decided to separate with Naruto going on to look for the villagers and Hinata and Sakura going back to get help. Amaru, who was supposed to go with Sakura stays to help Naruto. They then found some old ruins in which Shinnou mentioned earlier and enters the ruins. Shinnou is 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 Shinnou laughs at Amaru for trusting him. Shinnou tells that he's been researching on the power of darkness for about 15 years and he's finally found it in Konoha now he only needs secret scroll with a reincarnation jutsu or something written on it. He then transforms into a huge hulk-like creature with Naruto charging towards him only to be outmatched again and again beating Naruto badly.
Shinnou in the hulk-like form also tries to convince Naruto to use the Nine-Tailed Demon Fox's chakra with Amaru lost in tears while Shinnou and Naruto duke it out. Eversince she was small she had a weird illness and nobody liked her, fearing that they'll be infected, only Shinnou cared for her and managed to cure her. Naruto tells her not to throw her feelings away while evil Shinnou mocks her. She finally admits her love and feelings to which Shinnou just laughs and Naruto lands a hit. Sasuke appears suddenly saying "Orochimaru needs help with a reincarnation jutsu" to Shinnou and Shinnou gives him a scroll saying that's enough of help. Sasuke attacks with Chidori Senbon which attacks Shinnou's cells and he turns back to normal, who then flees the scene and Sasuke after him. Naruto tells Amaru to go find the villagers while he goes after Sasuke. He finds Sasuke in a room and asks him "What are you doing here?". In the same room is a cocoon which is absorbing dark chakra, Shinnou fuses with the cocoon and attacks Naruto and Sasuke. With tentacle arms Shinnou tries to absorb their chakra, Sasuke turns to Curse Seal level 1 and releases evil chakra and Naruto who got Sasuke's plan turns to his Nine-Tailed Demon Fox form sending a lot of chakra to the absorbing Reibi, breaking free with Shadow Clones before using Tornado Rasengan. After breaking free, Sasuke ascends to Curse Seal Level 2, using Chidori to cut off the beast's power, only for the creature acts on its own now after absorbing Shinnou.
In the meantime, Konoha successfully infiltrates the Sora-nin's base. Amaru finds Hinata and the villagers in a cell and frees them all and going off in lifeboats. Naruto appears again and orders Amaru to go, she refuses and Sasuke throws her in by force. Naruto also forces Sasuke onto the lifeboat with Rasengan, mouthing a few words to Sasuke as he falls before escaping. Remembering Jiraiya once said that Naruto had the willpower to never give up, he creates a large amount of Shadow Clones and starts to destroy the ruins, using Guts Rasengan. Soon, the whole ruin is destroyed with a Rasengan, leaving Naruto to fall down to the sea. Amaru, from a distance sees Naruto and grabs a pair of Sora-nin wings and goes for him upon reaching him, she grabs him and they fall together. Jiraiya suddenly pops out with Gamabunta and catches the two saving them.
Later on, Naruto wakes up in Amaru's arms with Sakura and Hinata are jealous at him. Sasuke goes back and gives Orochimaru the scroll, who then asks if something good had happened. Sasuke then goes off to train and remembers Naruto's whisper "I'll definitely bring you back to Konoha." "Sasuke!"