After being falsely accused of attempting to assassinate the leader of Kumogakure, the Raikage, and killing jōnin from Kirigakure and Iwagakure, Naruto is imprisoned in Hōzukijō, a criminal containment facility also known as the Blood Prison. The master of the castle, Mui, uses the ultimate imprisonment jutsu to steal power from the prisoners. In this place, something is aiming for Naruto’s life. The battle to prove his innocence and uncover the truth has begun for Naruto and his friends.
Following the invasion of Pain, leaders of the Land of Fire and Konoha gathered for an emergency meeting. Danzō convinced the daimyō that each of the previous Hokage had passed on a peaceful ideology to their students. This in turn made them too soft on military issues, resulting in Konoha’s destruction. The village now needed a strong and firm leader who would enforce the laws of shinobi and bring order to the world. He stated that he alone was fit to be Hokage. After brief consideration, the daimyō agreed to appoint him as the Sixth Hokage Candidate.
After Madara's revelation, Sasuke's new goal is to kill Danzo at the Five Kage summit. Meanwhile in Konoha, Karui, who thinks her master Killer B was captured by Sasuke, tries to beat out that information out of NAruto, who refuses to tell her anything. Sai intervines and stops her.
The Kages and their bodyguards are introduced as they embark to the Kage Summit, with Danzo revealing a little secret along the way. Naruto, Yamato and Kakashi tail Team Samui to meet up with the Raikage en route to the summit, while Taka and Zetsu arrive at the summit's location to find Danzo.
The Raikage continues to the summit after declining Naruto's request to call off the hunt for Sasuke. Sai is following his own plans and for the first time ever Sasuke is seeing Danzo. Also Danzo is made the heaed of the allied Shinobi forces by the summit.
After Mifune's proposal that Danzo should lead the allies forces, chaos breaks out at the summit. Danzo seems to have a secret.
Shikamru asks Sakura, if she agrees to take actions against Sasuke.
Yamato and Kakashi seem to have trapped Madara, who then shares Itachi's story with them and Naruto. A and his bodyguards start battling Sasuke and Taka.
Madara continues to tell the story of the Itachi clan and the Sage of the Sixth Paths to Naruto, Kakashi and Yamato. Sasuke is fighting the Raikage and A, activating Susanoo. Gaara intervenes and tries to draw Sasuke back to the light but fails.
Having blocked the combined attacks of Gaara, Temari, Kankuro, and Darui with his Susanoo, Sasuke goes after Danzo.
Madara Uchiha brings back Sasuke on his shoulder and wants to preach about his project Tsuki no Me. Lord Raikage is not handing the world to Madara. Gaara still wants to work on achieving peace, but there is no time for discussions.
KIller B is fighting with Kisame. Naruto gets to know from Sakura that she loves him. But her statement of giving up on Sasuke makes him distrust her. Sasuke, Sai and Kiba go after Sasuke themselves.
Killer Bee engages in a deadly battle against Kisame, who has come to capture the Eight-Tails.
Naruto learns the truth behind Sakuras confession, Madara makes quick work of Danzos subordinates, and the stage is set for the Sasuke vs. Danzo fight.
The Sasuke vs Danzo fight continues. Sasuke kills Danzo several times with Susanoo and Amaterasu, but Danzo always reappears using an unknown jutsu. Then Itachi appears behind Danzo.
Danzo’s uncanny jutsu prevents Sasuke from landing a clean hit on his enemy. As Karin attempts to analyze Danzo’s jutsu, Madara recognizes it as Izanagi.
Danzo believes he’s won the battle against Sasuke. Little does he realize, Sasuke placed him under genjutsu before they last exchanged blows.
Having tracked down Sasuke’s whereabouts with Kiba’s nose, Sakura attempts to put her allies to sleep and carry out the task of killing Sasuke herself.
Memories from his childhood course through Naruto’s mind as he rests to recover from his hyperventilation.
Sakura tells Sasuke that she wishes to desert the village and join him. A skeptical Sasuke tells Sakura he will believe her if she can finish off Karin.
Naruto reproaches Sasuke for attempting to kill Sakura. Then Sasuke reveals that he killed Danzo with his own hands. He goes on to declare his intent to purify the Uchiha clan’s name by annihilating the Hidden Leaf.
Years ago at the Final Valley, Sasuke told Naruto about high-level shinobi being able to understand one another just by trading blows. Having become a high-level shinobi, Naruto is now able to understand Sasuke’s heart.
Killer Bee returns to the Hidden Cloud Village to the delight of Omoi and Karui. He has brought Kisame’s sword, Samehada, with him. Bee believes the sword has taken a liking to him but is unaware that this is all just part of the Akatsuki’s plan.
Kakashi sends his ninken out to inform the other villages of Danzo's death while the feudal lords of the 5 Great Nations officially approve of the Shinobi Alliance. The Kages return to their respective villages and begin making preparations for the war.
Naruto gathers his friends and tells them that he will defeat Sasuke alone. Meanwhile, the Elders of the Leaf officially nominate Kakashi to become the next Hokage.
In Mount Myoboku, Gerotora, Fukasaku, and the Great Lord Elder are debating whether to give Naruto the key to the Tetragram Seal left behind by Jiraiya, an act that could unleash the Nine Tails.
At Mount Myoboku, Naruto prepares to store Gerotora within himself, but hesitates as it also holds the potential risk of unleashing the Nine Tails on the world.