As Sasuke rests from his battle with Deidara, the Leaf ninja pick up on his trail. Noticing that they're being followed, Karin tries to send them in the wrong direction while the members of Team Hebi head to the nearest Akatsuki hideout in hopes of finding Itachi. What will happen when Naruto and Sasuke have separate encounters with Itachi?

An ostrich tells a story of when Naruto, Rock Lee, and Shino, all led by Kotetsu, entered the Leaf Village's animal district in an effort to find and subdue him. However, he and the other animals proved that they weren't willing to go down without a fight.

The four Kage are startled by the sudden appearance of Madara Uchiha. Having sent Sasuke away to safety using the Transportation Technique, Madara unveils to the Kage his “Project Tsuki no Me.”

Kakashi rescues Sakura from certain death at Sasuke's hands and takes over the fight. After healing Karin, Sakura again decides to take on Sasuke, but her resolve fails her. Just as she comes close to death a second time, Naruto intervenes and saves her. After so long, the original Team 7 is reunited.

Tsunade talks to a council and informs about the Fourth Shinobi World War and warns others not to underestimate Akatsuki. Whereas in Land of Lightning a council is held about war, as Kisame spies on them. B paying no attention was bought in writing raps in his rhyme book. Later, Shizune informs Tsunade about Naruto's disappearance for which she ordered some shinobi to search for him. Naruto returns to Ramen Ichiraku. Two Konoha shinobi ask for his autograph, but he doesn't know how to respond. Three days later the Kage meet again to discuss how they should start pooling their resources. As the first matter of business, Naruto and Killer B are to be given constant protection. Tsunade objects since they would both be invaluable in the war with Akatsuki, but is forced to agree. Tsunade meets with A alone and asks him for a favour to let B teach Naruto how to control Nine-Tails. A says that the place where he is sending B and Naruto isn't just a hideout but a training ground. Tsunade returns to the village and informs Naruto that he's going on an S-rank misson to an island located in the Land of Lightning.

Making a stop at a nearby port to stock up on supplies, Naruto buys a rare mushroom from a vegetable merchant. But soon after they set sail for their next destination, Naruto and the other crewmembers find their ship infested with poisonous mushrooms.

Kakashi races to the scene where the Seven Ninja Swordsmen Kushimaru Kuriarare and Jinpachi Munashi were last sighted. Enraged by the carnage they’ve left behind, Kakashi teams up with Might Guy.

Itachi uses the ultimate genjutsu technique Koto Amatsukami to free himself from the Reanimation Jutsu. Itachi then joins Naruto and Killer Bee to fight Nagato, who is still under Kabuto’s control.

Yugao is ordered by Sukui to track down the reanimated Hayate. Still shaken by her lover’s unexpected return as an enemy, Yugao manages to catch up to Hayate and his men.

Casting aside Itachi's lectures to him, Kabuto reveals to the siblings that he had injected himself with the DNA of various shinobi, namely the Sound Five, also including Orochimaru.

The fighting rages between Naruto, who stands at the vanguard of the Allied Shinobi Forces, and the team of Madara and Obito.

With his newly revived strength, Madara doesn't give in against the nine Tailed Beasts.

It’s been two years since the end of the Fourth Great Ninja War. Shikamaru now has an important role within the Hidden Leaf government, and as a representative of the Leaf in the Alliance. One day, a situation develops with shinobi disappearing in droves, and Shikamaru takes on a dangerous mission.

Ino, Choji, and Temari rush to Shikamaru’s aid! Choji takes on Ro, Temari goes after Soku, and Ino goes after Sai! Meanwhile, Shikamaru pursues Gengo. Can Shikamaru defeat Gengo’s evil ambitions? The final battle begins!