Two years after the events of the Fourth Great Ninja War, the moon that Hagoromo Otsutsuki created long ago to seal away the Gedo Statue begins to descend towards the world, threatening to become a meteor that would destroy everything on impact. Amidst this crisis, a direct descendant of Kaguya Otsutsuki named Toneri Otsutsuki attempts to kidnap Hinata Hyuga but ends up abducting her younger sister Hanabi. Naruto and his allies now mount a rescue mission before finding themselves embroiled in a final battle to decide the fate of everything.

After his capture for attempted assassination of the Raikage, leader of Kumogakure, as well as killing J?nin from Kirigakure and Iwagakure, Naruto is imprisoned in H?zukijou: 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.

Sixteen years ago, a mysterious masked ninja unleashes a powerful creature known as the Nine-Tailed Demon Fox on the Hidden Leaf Village Konoha, killing many people. In response, the Fourth Hokage Minato Namikaze and his wife Kushina Uzumaki, the Demon Fox's living prison or Jinch?riki, manage to seal the creature inside their newborn son Naruto Uzumaki. With the Tailed Beast sealed, things continued as normal. However, in the present day, peace ended when a group of ninja called the Akatsuki attack Konoha under the guidance of Tobi, the mysterious masked man behind Fox's rampage years ago who intends on executing his plan to rule the world by shrouding it in illusions.

A mysterious group of ninjas makes a surprise attack on the Konohagakure, which takes great damage. The nightmare of another Shinobi World War could become a reality. Sasuke, who was still a missing nin from Konoha trying to kill his brother, Itachi, appears for the second time in front of Naruto at an unknown location to prevent it from happening.

Ichigo Kurosaki's school is attacked by strange spirits called Unforgiven (Togabito), revealed to have escaped from Hell, and Rukia Kuchiki and Renji Abarai are sent to investigate. Ichigo's family is targeted by the Unforgiven, who are led by Shuren, and Ichigo's younger sister Yuzu Kurosaki is abducted. An Unforgiven named Kokut? saves Karin Kurosaki from being abducted as well, and convinces Ichigo to accompany him and the Soul Reapers to Hell to save her. When they are attacked by monsters called Kushan?da, the guardians of Hell, on the journey, Ichigo's Hollow mask begins to spontaneously manifest. Kokut? warns him to avoid using his mask lest he lose control and hollowfy entirely, and tells him that the Kushan?da torture Unforgiven for their sins by killing them, as Unforgiven continuously revive, and that spirits killed in Hell become Unforgiven themselves.

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.