Fated Battle Between Brothers

The Fated Battle Between Brothers is from Part II of the series, spanning from chapter 383 to chapter 412 and episodes 138 to 143. This arc details the continuation of Sasuke's battle with his brother Itachi along with its aftermath and Sasuke's meeting with Tobi. This arc is preceded by the Tale of Jiraiya the Gallant. It is followed by Pain's Assault in the manga and Tsuchigumo Kinjutsu Arc in the anime.

Sasuke vs. Itachi
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 Technique, and Sasuke held a slight advantage until Itachi used Amaterasu, which burnt out Sasuke's fireball immediately, and melted through his remaining cursed 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, 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 technique was unavoidable. Zetsu continued watching the fight, narrating their movements and adding background to mysterious moves. Sasuke charged his final technique, Kirin. A huge creature made of lightning appeared, fuelled by the Great Dragon Fire Technique which had dumped a huge amount of residual heat into the upper atmosphere, and Sasuke's chakra remained suspended in a usable form, changing with the atmosphere from simply fire chakra into a bolt of lightning characterised in the same form as the earlier Great Dragon Fire Technique, but cast instead from lightning. Sasuke hit Itachi, who appeared to be dead. Itachi was then shown to be alive somehow, and revealed a third Mangekyō technique: Susanoo, which pulled out the legendary Sword of Totsuka. Giant snakes suddenly appeared out of Sasuke. One of them revealed Orochimaru inside its mouth. Sasuke, having used up nearly all of his chakra fighting Itachi, could no longer suppress Orochimaru, who had been inside of Sasuke since his failed attempt at taking over his body. The snakes were all killed, and Orochimaru was stabbed by the Sword of Totsuka, sealing him in an eternal dream state, and the remains were subsequently sucked into the Sake jar that the Sword of Totsuka was sheathed in. Itachi then asked Sasuke if that was all he had. Sasuke then proceeded to attack Itachi, again ending in a futile attempt as all his attacks were reflected by another effect of Susanoo, the Yata Mirror, which reflected all attacks directed at Itachi. Sasuke was knocked back by his own attacks, and laid on the ground. Itachi seemed to be invincible, when Susanoo began to fade. Itachi walked towards his brother, seeking his eyes. When Itachi reached Sasuke, he poked Sasuke's forehead, saying, "I'm sorry, Sasuke. There won't be a next time", a reference to his constant unfulfilled promises to train with Sasuke in their youth. Itachi then died of exhaustion. Zetsu figured that Itachi must have been injured before the battle started, also noting that Itachi was unable to dodge attacks he would normally be able to. Sasuke then smiled and closed his eyes before collapsing himself, as Itachi's Amaterasu continued to burn around them.

Meanwhile, Naruto and the other members of the Eight Man Squad continued to fight Tobi. Shino attacked with his bugs, and even managed to completely swarm Tobi with them. Tobi escaped from the swarm unharmed, however. Zetsu arrived to tell him that Sasuke had won the battle, and that Itachi was dead. This was no surprise to Tobi. Zetsu also said that Sasuke was probably dying as well. Just before Tobi and Zetsu left, Kakashi noticed Tobi's Sharingan. Kakashi commented on this while Tobi and Zetsu fled to the battle-site. Hinata saw storm-clouds and the flames of Amaterasu with her Byakugan. Naruto and the group pursued them. Meanwhile, Tobi and Zetsu reached Sasuke. Tobi told Zetsu to take Itachi's corpse. Naruto's team reached the flames, and Yamato used Earth Release: Earth Flow Divide to create a path through it. Naruto became angry when he realised that they were too late.

The Truth About the Uchiha Clan
Sasuke woke up in a large room. Tobi appeared from the shadows, and said that he would tell Sasuke "the truth" about Itachi. He then began to take off his mask. As Tobi's, whose true identity is none other than Madara, Sharingan was shown, Sasuke's Sharingan was turned into Mangekyō Sharingan. His eyes bled, and Amaterasu appeared around Tobi. Tobi said that Itachi had implanted his abilities into Sasuke, and that they would activate as soon as Tobi's Sharingan was shown. Tobi then said that Itachi had done this to kill Tobi, and to protect Sasuke. Sasuke didn't believe him, and yelled at Tobi to go away. Tobi then began to tell Sasuke the secret, about how Itachi had tried to protect the village as well as Sasuke, but for things to make sense, he would have to go back before the founding of Konoha.

At the time, there were many clans that existed, and the Uchiha clan was one of the strongest, only to be rivalled with the Senju clan whom they constantly battled. Madara was noticed as the leader of the Uchiha clan because of his powerful chakra, but as Itachi said before, Madara plucked out his brother, Izuna's eyes so he can gain an Eternal Mangekyō Sharingan. In order to end their fighting, Hashirama Senju, the leader of the Senju clan, decided to make a peace offering with the Uchiha, which had formed the village of Konoha. Madara became infuriated when Hashirama became the First Hokage because he feared that the Uchiha clan would be put down, but the Uchiha did not believe their leader's warning, so Madara decided to abandon his own clan and defect from Konoha. Madara used the power of his Eternal Mangekyō Sharingan to take control of the Nine-tails to take his revenge and battled Hashirama which tore up the landscape and this land would eventually be called the Valley of the End, the same place where Sasuke battled Naruto before he left Konoha. At the end of the battle, Madara lost control of the Nine-tails and everyone, even the Uchiha and Hashirama believed Madara had died. Afterwards, little by little, the Uchiha clan began losing their power as the village recognised the Senju clan more, and everything Madara had warned his clan about was beginning to come true, when the final straw occurred. 16 years ago, the Nine-Tails attacked Konoha, and due to the Uchiha's reputation back when Madara controlled the Nine-Tails against his fight against Hashirama, the leaders of Konoha believed the Uchiha were responsible. In punishment, the Uchiha were forced to live in one area.

Itachi was ordered by the elders of Konoha to annihilate the Uchiha because they were planning a coup d'état against Konoha, and Itachi had done this because he detested war, and wanted to maintain Konoha's stability. When Itachi was not even four years old, he had seen the bloodshed of the Third Shinobi World War which caused him to develop a pacifist nature. Coincidently, Tobi was attempting to destroy Konoha when he encountered Itachi, so Itachi made a deal; If he were to help Itachi wipe out their clan, "Madara" must leave Konoha alone, which Madara accepted. Sasuke began to believe Tobi was the real bad guy because Itachi said that Madara was controlling the Nine-Tails' every move, but "Madara "denies his involvement and Itachi only said that because he did not want Sasuke to trust Madara. This triggered a flashback to moments before Itachi's death; revealing that he was not seeking his brother's eyes, but, in his final stance with Sasuke, had poked him on the forehead (as he did in Sasuke's childhood) and smiled at him. After this, Sasuke was shown joining back up with Hebi with his new Mangekyō Sharingan. He told the group that they would be called Taka from now on, and that their goal was "the complete and utter destruction of Konoha".

Decoding the Message
After the failed mission to find Sasuke or Itachi, Naruto remembered his encounter with Itachi. Itachi asked Naruto why he insisted on trying to save Sasuke who doesn't want to be saved, and Naruto replied he was more a brother to him than he ever was. Satisfied with his answer, Itachi departs, but not before performing a technique on Naruto, to prepare him for the chance that Sasuke attacks Konoha. Soon after, Naruto is called to the Hokage office where he is told by Fukasaku, that Jiraiya was killed in Amegakure by Pain. Naruto, devastated, left to mourn while Tsunade, who was equally hurt, has the decoders decode Jiraiya's dying message on Fukasaku's back.

Devastated and unable to focus even after encouraging words from Iruka Umino, Naruto was taken by Shikamaru Nara to the hospital to see a pregnant Kurenai Yūhi, whose child Shikamaru will instruct. Shikamaru reminded Naruto that there will come a time where all their masters will be gone and they will be the new masters of new students. With this in mind, Naruto opts to help the decoders decode the message, and saw that the message was written in Jiraiya's unique, if somewhat sloppy katakana script. With this knowledge, they discover Pain's secret that "The real one isn't there". After deciphering the code, Fukasaku asks that Naruto come with him to learn senjutsu like Jiraiya.

After a Reverse Summon sent Naruto and Fukasaku to Mount Myōboku, the two began the difficult senjutsu training. The training required Naruto to first be completely still so to allow himself to mould the natural chakra surrounding him. To speed up the process, special frog oil was smeared on Naruto that would allow him to use natural chakra, but at a higher risk of turning into a toad statue. After several days to weeks, Naruto successfully learned how to remain perfectly still in order to mould enough natural chakra to enter Sage Mode, and even trained himself in secret to master his Wind Release: Rasenshuriken. However, when time came to learn Sage Art: Amphibian Technique to allow Shima and Fukasaku to gather the natural chakra while in combat, the Nine-Tailed Demon Fox prevented the fusion requiring Naruto to come up with an alternative method of entering Sage Mode in battle.

Taka Confronting the Eight-Tails Jinchūriki
Meanwhile, Sasuke decided to not take Itachi's eyes to awaken his Eternal Mangekyō Sharingan, opting to restore their clan his own way. Tobi ordered Taka to find the jinchūriki of the Eight-Tails, Killer B of Kumogakure. They find him at the Valley of Clouds and Lightning and begin to battle. Taka proves to be a challenge to B, and he proceeds to go all out.