Senjutsu Training arc

The Senjutsu Training arc is from Part II spanning from chapters 403 to 418 of the manga. Portions of this arc is sometimes divided into separate smaller arcs, all of them leading up to Pain's invasion of Konoha and its aftermath.

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. Satified with his answer, Itachi departs, but not before preforming a jutsu on Naruto, to prepare him for the chance that Sasuke attacks Konoha. Soon after, Naruto is called to the Hokage Residence where he is told by Pa Toad, 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, Shikamaru Nara took Naruto to the hospital to see a pregnant Kurenai Yuhi, who's 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 is knoweledge, they discover Pain's secret that "The real one isn't there". After decifering the code, Fukasaku asks that Naruto come with him to learn Senjutsu like Jiraiya.

After a Reverse Summon sent Naruto and Fukasaku to Myōbokuzan, the two began the difficult Senjutsu training. The training required Naruto to first be completely still so to allow himself to mold 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 mold 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.

Sasuke and the Eight-Tails
Meanwhile, Sasuke decided to not take Itachi's eyes to awaken his Mangekyō Sharingan, opting to restore their clan his own way. Madara ordered Taka to find the Jinchūriki of the Eight-Tailed Giant Ox, Killer Bee of Kumogakure. After finding him at the Valley of Clouds and Lightning and quickly began to battle. Killer Bee however easily disarmed Suigetsu Hōzuki, and defeats Jūgo with Suigetsu's own sword. When Sasuke challenged him alone, despite using his Mangekyō Sharingan, Killer Bee was able fatally injure Sasuke twice, first when he was stabbed multiple times by Killer Bee's swords, from which he was saved by Karin sucking her chakra, after taking a hit from three-tailed Killer Bee's Lariat, blowing open his chest, he was saved by Jūgo infusing his cursed flesh with Sasuke's body.

Annoyed, Killer Bee fully transformed into the Eight-Tailed Giant Ox. Suigetsu tried to blow Killer Bee away with a giant wave, but was easily repelled by a concentrated ball of chakra. Out of desperation, and seeing Taka resemble his former team, Sasuke used Amaterasu to stop the giant ox. Using this opportunity, Saskue cut off one of the beasts tentacles, but it hit Karin, causing her to ignite. Sasuke managed to put the flames out on her, and the Killer Bee. After collecting the injured and their captive, Sasuke and Jūgo head back to to Akatsuki's base.

When Sasuke delivered Killer Bee to Madara, he informed him that his true intentions was to not destroy Konoha's elders, but the entire village for making the Uchiha destroy themselves, vowing to destroy anyone who gets in his way. His goal completed, Sasuke departs to Taka's hideout, unknown they were followed by Kumo-nin Jei. When he was discovered, he was quickly killed by Taka before they retreat.

During the sealing of the Eight-Tails, which was taking longer due to losing most of their members, Killer Bee's body turns back into a tentacle mid-sealing. Killer Bee, still at the battlefield, climbs out of a tentacle at the bottom of the lake, relieved that Akatsuki "kidnapped" him and allowed him a chance to leave the village.