Tsunade continues to read Jiraiya’s novel. Chunin- and jonin-level ninja have gone missing, and the Fourth Hokage, Minato, orders a search mission with teams of genin led by Guy and Kurenai. Kakashi’s Team 7 is also dispatched, but the hero Naruto Uzumaki, despite being the Hokage’s son, has the misfortune of being labeled a loser.

Sasuke has left with Orochimaru, but Naruto is not about to give up. Determined to bring Sasuke back, he returns to the village with Shikamaru and the others. Meanwhile, Yahiko appears in the village, calling himself “Pain" and seeking revenge for the Hidden Leaf’s betrayal.

After the Great War, many missing and Rogue Ninja made their way into the Land of Silence. Sai, who has infiltrated the region to investigate, sends a cryptic message back to the Leaf. Shikamaru, determined to find out what's happening, heads for the Land of Silence with two members of the ANBU, Soku and Ro. However, they must first get past a heavily guarded checkpoint.