Ninjas with bloodline limits begin disappearing in all the countries and blame points toward the fire nation. By Tsunade's order, Kakashi is sacrificed to prevent an all out war. After inheriting charms left by Kakashi, Naruto fights through friends and foes to prevent his death while changing the minds of those who've inherited the will of fire.

Assigned on a mission to capture Mukade, a missing-nin, Naruto Uzumaki sets out for the once glorious historic ruins of "Ouran", where he pursues and corners the rouge ninja. Mukade's goal is revealed to be a dormant leyline within the ruins; he unleashes the power of the leyline, causing a light to envelop Naruto, sending him into the past, 20 years before the series began. When Naruto awakens, he comes into contact with the Fourth Hokage, Minato Namikaze.

After his capture for attempted assassination of the Raikage, leader of Kumogakure, as well as killing Jōnin from Kirigakure and Iwagakure, Naruto is imprisoned in Hōzukijou: A criminal containment facility known as the Blood Prison. Mui, the castle master, uses the ultimate imprisonment technique to steal power from the prisoners, which is when Naruto notices his life has been targeted. Thus begins the battle to uncover the truth behind the mysterious murders and prove Naruto's innocence.