Mangekuo

At Orochimaru's lair, a sick Orochimaru was confined to his bed. As Kabuto exited to get more medicine, a blade made of lightning chakra shot towards Orochimaru through the door. Orochimaru quickly blocked it with his arms, and thought to himself that he did not recognize the shape manipulation, although the chakra itself seemed familiar. The blade belonged to Sasuke, who had stopped by to finish Orochimaru off before he left to take on Itachi. He claimed that he had nothing more to learn from Orochimaru. Then continued by mocking him for wasting his power and time, which angered Orochimaru.

After pinning Orochimaru's arms to the wall, Sasuke attempted to deliver a finishing blow, forcing Orochimaru to abandon his body and reveal his true form: a composite serpent-like entity made up of small white snakes. Sasuke activated his Cursed Seal Level 2, and began to fight Orochimaru. He compared Orochimaru's ambitions to how a snake dreams of flying, and told him that he would only get that chance in the talons of a hawk, as he sprouted his Cursed Seal wings.

After he severed Orochimaru's head from his body, Sasuke believed he had won. However, Orochimaru's poison paralyzed Sasuke, and the former then lunged at him, swallowing him whole. Sasuke found himself inside Orochimaru: the place where the body-transfer jutsu took place. Orochimaru relived a flashback of when he confronted Itachi while in Akatsuki. He found Sasuke's eyes to be similar to those of Itachi's on that day, and anticipated taking possession of those eyes. However, Sasuke took over the dimension with his Sharingan and Cursed Seal, and proceeded to turn the jutsu against Orochimaru. After the fight, Kabuto returned with the medicines, but viewed a scene consisting of Sasuke standing over Orochimaru. Kabuto asked Sasuke which one he was, to which Sasuke replied by showing Kabuto what had happened. Sasuke stated that he had merely taken over.

At the start of the series, one of the only techniques Naruto could do without fail was the Transformation Technique, and his own original variant of the technique called the Sexy Technique; a creative but almost completely useless diversionary jutsu, used simply to shock his instructors.[11] Naruto was also able to use simple E-rank abilities.
While under the tutelage of Jiraiya, Naruto's abilities had continued to improve; his prowess in ninjutsu and taijutsu had grown greatly, and he had also been taught some limited skill at dispelling genjutsu. However, the most valuable assets that Naruto had gained in his training with Jiraiya were an increased range of battle smarts and more knowledge of the basics of a shinobi, which he lacked during Part I. This, along with the skills and abilities Naruto has gained over the course of Part II, makes him a much more complete ninja. Unfortunately for him, with the exception of the Wind Release: Rasenshuriken and throwing himself with clones (which are both risky moves), he is mainly limited to short-range combat. However, with his mastery of the Chakra Arms, he has a new method for attacking long-ranged.
During Part II, Naruto had regularly proven himself a match against the S-rank members of Akatsuki, Deidara acknowledged how strong he had become, even landing a blow on him; he was able to defeat Kakuzu using a clever strategy and his new Rasenshuriken; and later defeat all of Nagato's Six Paths of Pain, something no one else had ever accomplished. It had been said by Kakashi at different points in time that Naruto had surpassed Kakashi himself, Jiraiya, Tsunade, and his father. He was suggested to be Hokage in Tsunade's place by several villagers following Pain's invasion. Zetsu had noted that Naruto was stronger than Sasuke following Pain's invasion. Even the Nine-Tails, the strongest of the tailed beasts, commented on how powerful Naruto had become when they battled.
Being a descendant of the Uzumaki clan, Naruto possesses incredible stamina and vitality, the former of which is further augmented by the Nine-Tails sealed within him, and he apparently has some knowledge on fūinjutsu, as he knew how to use the key to undo and redo his seal after receiving Gerotora. Jiraiya had left Naruto with the key to help him complete an unknown technique which he, Naruto, and Minato have been working on, but never finished. Naruto stated that he was ready to complete it.
While searching for the Uchiha brothers, Itachi granted Naruto a portion of his power, in case Sasuke ever chose to revolt against Konoha. It is currently unknown what this power is yet.

Sasuke arrived at the Uchiha hideout, and confronted Itachi. The battle began with both of them seemingly using Taijutsu, soon ending with Sasuke cornering Itachi and deciding to ask him one last question before killing him off. Sasuke asked, "Who is he?" Sasuke recalled when Itachi had said that three of the Uchiha clan would have the ability to use the Mangekyō Sharingan, including himself, if Sasuke would be able to awaken his. Itachi explained that the person who had assisted him when he murdered the entire clan was none other than Madara Uchiha, one of the founders of Konoha, and revealed that one of the purposes of the Mangekyō Sharingan was to control the Nine-Tailed Demon Fox which he had done 16 years ago when it attacked Konoha. He also revealed that, once the Mangekyō Sharingan was activated, it would progressively lead to blindness. Itachi referred to Madara is the founder of Akatsuki and his mentor. It then turned out that Sasuke and Itachi's battle so far had been pure genjutsu. Itachi then finally activated his Mangekyō Sharingan, and revealed that the only way to stop the blindness was to take the eyes of another Sharingan user; he stated that this was the reason he had left Sasuke alive, and why he had pushed him to become stronger. After a flashback of his childhood, Sasuke stated, "Finally ... it all ends here." During their talk, Zetsu watched hidden from the ceiling, and his halves began to comment on the battle.

After securing him in place with a Shadow Clone, Itachi then proceeded to rip out Sasuke's eyes. It was revealed that the whole fight so far had been a genjutsu, namely Itachi's Tsukuyomi, which Sasuke had overcome.

Sasuke shortly lectured Itachi about the tools of the ninja, and how a tool was only as powerful as the ninja who used it. Itachi told Sasuke that he would make his dream, of ripping out his eyes, a reality, and readied the Amaterasu. Itachi and Sasuke both used the Great Fireball Jutsu, and Sasuke held a slight advantage until Itachi used Amaterasu, which burnt out Sasuke's fireball immediately, and melted through his remaining Curse Seal Level 2 wing, as well as scorching his body. Itachi prepared to rip the eyes out of the half-burned Sasuke, but the corpse was shown to be an empty shell left behind by Orochimaru's Kawamari (Shedding Skin) Jutsu, and the real Sasuke had dropped into the floor below. He used a new ninjutsu, named Fire Release: Great Dragon Fire Technique, from down below. Itachi dodged, but it still burnt his arm. Soon it began to rain, and Sasuke said that this new jutsu was unavoidable. Zetsu continued watching the fight, narrating their movements and adding background to mysterious moves.

Tsunade returns to Konoha as the new Hokage. The villagers are eager to have her begin her official duties, but Naruto insists that she help Sasuke and Kakashi first. They run into Shikamaru along the way, who, given his history with women, is unhappy that the Hokage is a woman too. He later reluctantly has lunch with Team 10 to celebrate his appointment as a chūnin, the only advance in rank from the Chūnin Exams. Neji elsewhere tries to locate birds with his Byakugan, but can only see seven of eight. Tsunade heals Kakashi and Sasuke. Sakura is particularly happy with Sasuke's recovery, having stayed by his bedside since his encounter with Itachi. Guy pleads for Tsunade to look at Lee too.

Tsunade examines the damage to Lee's back and finds there are bone fragments lodged in his spine. Although she, and only she, could try removing them, Lee will die if she fails. Since her odds of success are only 50%, she advises he give up his dreams of being a ninja. To Guy's disappointment, Lee accepts his prognosis and leaves. While Team 10 is having lunch, Chōji insists that he get to have the last morsel of food, claiming it is the best. Asuma points out that he should train more and become a chūnin like Shikamaru, upsetting him. Sasuke, still recovering from his encounter with Itachi, thinks about how useless he was and how much Naruto has surpassed him. Orochimaru elsewhere sends his Sound Four to Konoha.

Naruto thinks about his lunch with Iruka. Iruka is happy with Naruto's development, but informs him that he will now need to start doing actual work. After the failed invasion of Konoha, the village is operating with a diminished manpower and ninja are being sent on more difficult missions and more often. Naruto is eager to start doing his part. After Team 10 has lunch, Ino tells Shikamaru that Chōji should go on a diet. Shikamaru defends him. Chōji tells Shikamaru that, now that he is a chūnin, his superiority to Sasuke and Neji is only more apparent. Shikamaru is unconcerned since he only wants to be himself, which he tells Chōji to strive for too. Naruto visits Sasuke in the hospital. Because so many others have shown a special interest in Naruto, Sasuke demands that they fight each other. Naruto accepts.

Over Sakura's objections, Naruto and Sasuke head to the hospital roof to fight. Regarding the battle casually, Naruto asks Sasuke to put on his Konoha headband. Sasuke refuses since that would mean that they are equals, upsetting Naruto for not acknowledging himself as Konoha ninja. Naruto surrounds Sasuke with shadow clones, which Sasuke destroys with his Fire Release: Great Fireball Technique. As the smoke clears Sasuke sees that one clone has survived and is helping Naruto form the Rasengan. He uses his own Chidori and they charge at each other. Sakura screams for them to stop.

After Killer Bee refused to train Naruto, Motoi guided Naruto and Yamato to the Falls of Truth, the place where Bee trained to control the Eight-Tailed Giant Ox. He instructed Naruto to sit on a platform and close his eyes. Soon after, Dark Naruto (闇ナルト, Yami Naruto) appeared, berating Naruto for how quickly the people from Konoha changed their ideals of Naruto and had started sucking up to him, which sickened Dark Naruto.Dark Naruto said that he was the manifestation of hatred that existed within Naruto's heart, the Nine-Tails liked him better, and exclaimed that he was the real Naruto and that Naruto was an impostor.They started to fight, but after a while, Naruto realized that they both had the same techniques, skills, and tactics. As a result, their fight was a draw and Naruto mentioned that if they continued like this, it would take a long time to settle it, so he awoke and told Yamato and Motoi what happened. Motoi told him that he must defeat Dark Naruto in order to learn how to control the Nine-Tails.
He appeared once again after Naruto returned to the Falls of Truth. Instead of fighting, Naruto projected an image from his mind of his autograph signature he was unable to give to the Konoha shinobi. This angered Dark Naruto, pointing out to Naruto that those people were part of the same villagers who treated him as an outcast and how much he suffered because of them, telling him shouldn't trust them. However, Naruto stated that he trusts the villagers because they are important to him. But what was also important was that he needed to have faith in himself, so he would have the strength to live up to the villagers' trust in him. Naruto's statement started to weaken Dark Naruto, forcing him to ask what was the reason for his existence then. Naruto stated that Dark Naruto was really him and thanked Dark Naruto for pushing him to be the person he was now. He hugged Dark Naruto when the latter tried to attack him, telling Dark Naruto that it was all going to be alright. Letting go of his own anger at their past, Dark Naruto's eyes lightened and he gave into Naruto's words, disappearing into Naruto.
Later, when Naruto entered his subconscious, the Nine-Tails expressed surprise as it could no longer sense any hatred within Naruto, and questioned Naruto about where the "real him" was, to which Naruto replied that the real him was right in front of it.