The Leaf Village is left in ruins in the wake of Pain's assault on the village. While cleaning through the remains of Ninja Academy, Iruka finds an old pillar and recognizes it as a memoir from Naruto's early years at the academy.
Naruto spends his days competing with Sasuke, the academy's star student, only to screw up and be the laughingstock of the class. Due to the childhood trauma of losing his parents to the Nine-Tailed Fox, Iruka finds it difficult to interact with Naruto as his student.
An emergency council is held before the Feudal Lord of the Land of Fire. The topic is to discuss plans to rebuild the Leaf Village, and Danzo strongly urges the council to select a new Hokage to replace Tsunade.
The Leaf ninja work to rebuild the Hidden Leaf Village. While helping with the restoration, Naruto and Sakura are reunited with two old friends--the carpenter Tazuna and his grandson Inari from the Land of Waves.
Naruto visits Sakura, who is caring for Tsunade. Sakura recalls an incident that took place three years before, in which she collapsed from symptoms that resembled a disease caused by a mysterious virus.
After accidentally finishing off Lee's last special youth drink, Naruto asks Guy to make more, only to learn one of its key ingredients, the Jofuku Flower, is out of stock. Naruto is determined to get the Jofuku Flower for Lee's sake.
Naruto is assigned to a team led by jonin Hayama to patrol the north border of the Leaf Village. One of his teammates is Kosuke, an old man who has been a genin for over fifty years, earning him the title "Eternal Genin."