Naruto Uzumaki returns to Konoha after a two-and-a-half-year training journey with Jiraiya. He is reintroduced to his peers, who have advanced to at least Chunin rank, unlike Naruto who is still a Genin. Naruto know that Gaara become Kazekage of the Desert of the Sand who has since the village leader. Elsewhere, two members of Akatsuki head towards Sunagakure to capture Gaara.

When an artifact known as the "King's Seal" is stolen during transport from Soul Society, Hitsugaya Toushirou is assigned to retrieve it. Toushirou goes missing after a battle with the thieves, leading Seireitei to suspect him of treachery. They order his immediate capture and execution. Unwilling to believe him capable of such a crime, Ichigo, Rangiku, Rukia, and Renji set out to find Toushirou and clear his name. Meanwhile, Toushirou is still searching for the thieves, and stumbles upon a dark secret involving a shinigami long since dead.