Enemy ninjas from the Land of the Sky arrive in Konoha and quickly set about attacking the village by committing an act of vengeance for the Leaf Village's devastating attack on the Sky Country during the Second Great Ninja World War.
While Naruto Uzumaki, Sakura Haruno and Hinata Hyuga escort Amaru and Doctor Shinnō to their village, Sai and Shino Aburame destroy the sky ninja's ship base. Orochimaru, now suffering from his expired body, orders Sasuke Uchiha to get a man who can help him perfect his reincarnation. At the now burning village, Amaru searches for the villagers, with a trap seemingly killing Shinnō. After Amaru recovers herself and senses, the remaining allies continue trying to find the missing villagers.
After Hinata is separated from the team, Amaru is possessed by the Zero-Tailed monster, Reibi. Naruto nearly transforms into a tailed beast state, but the seal suppresses the Nine-Tailed Fox’s chakra within him and Amaru resists the power of Reibi. At the floating fortress Ancor Vantian, Naruto learns that the recovered Shinnō had betrayed them, using Amaru to research the power of darkness fifteen years ago, as well as the village's secret scroll. After Shinnō temporarily activates Body Revival Technique, Naruto stops Amaru from committing suicide.
Sasuke appears and intervenes, telling the weakened Shinnō to help Orochimaru, but Shinnō refuses, giving the reincarnation Jutsu scroll to Sasuke before falling into a trap door. Naruto and Sasuke confront Shinnō, revealing the giant cocoon to be the Zero-Tails and transforming into a chakra-absorbing monster. After Sasuke releases the curse mark and Naruto the fox's chakra, they overload Shinnō with charka, destroying him with the Lightning Blade and Tornado Rasengan. With the fortress no longer having power, Ancor Vantian falls. While several leaf ninjas attempt to infiltrate and destroy the fortress, Amaru, Hinata and the freed villagers prepare to leave.
After Naruto destroys the remaining fortress with the Rasengan (螺旋丸, lit. spiral sphere, English manga: "Spiral Chakra Sphere") and falls through the sky, Amaru rides on the glider to save him. They then land safely on Gamabunta.
Returning to the hideout and giving the scroll to Orochimaru, Sasuke continues training, reflecting on Naruto's last words to him.
