The Hidden Leaf is under attack from the Flying Ninja. They want to destroy all five great countries and create a single powerful empire, the Sky Empire. The Flying Ninja have attacked Konoha and caused great damage. Now it's Konoha's turn to counterattack, but Naruto is not involved in this attack and is sent with Sakura and Hinata to protect the doctor ninja Shino and his apprentice Amaru, who are traveling to Amaru's village. Naruto soon discovers that everything is more complicated than it seems and that all five shinobi nations could be destroyed.