News has spread throughout the Leaf Village that a cloaked man has stolen data from the archives. Team 10 decides to launch their own investigation to find and catch the thief.

Amado defects from Kara. Desiring to seek asylum in the Leaf Village, he takes Shikadai hostage. If granted asylum, Amado promises to provide the Leaf Village with every bit of knowledge that he has about Kara.

Amado reveals to Naruto and the others the knowledge that he possesses regarding Jigen, the Otsutsuki Clan, and Karma. Meanwhile, Koji Kashin confronts Jigen, and Amado's plan to eliminate him is revealed.

Koji Kashin continues his battle with Jigen, whose body is revealed to have been taken over by Isshiki Otsutsuki. He continuously hits Jigen with a barrage of attacks in an attempt to drag Isshiki out of his body and destroy him.

Isshiki regains his true form and goes to the Leaf Village to recapture Kawaki. The Leaf shinobi prepare for his arrival. Boruto is willing to fight, but he becomes frightened at the possibility of losing control of his Karma again.

Boruto opens a portal and transports Isshiki and himself to another dimension. Naruto and Sasuke follow them, and the final battle against Isshiki begins.

Naruto and Sasuke are greatly overwhelmed by Isshiki's abilities. As a last resort, Kurama offers Naruto a chakra mode called Baryon Mode, which grants him immense power. The intensity of this power, however, could end his life.

Naruto and the others are exhausted from their battle with Isshiki. Suddenly, Boruto attacks Sasuke. Momoshiki has taken control of Boruto’s consciousness and stands before them as an enemy. Kawaki desperately calls out to Boruto to snap him out of it. Unfortunately, his words are unable to reach him. Sasuke tells Kawaki a way to bring back Boruto’s consciousness. In order to save Boruto, Kawaki attempts a risky plan using a jutsu he only recently learned. While Kawaki and Sasuke fight a desperate battle, Naruto finally runs out of strength. As his consciousness fades, he and Kurama quietly reminisce about their past.

Finished with their battle against Isshiki, Boruto and the others return to the village. Thanks to their work, the safety of the village has been maintained. Boruto is terrified by the fact that Momoshiki once again took over his consciousness during battle. Meanwhile, Amado provides some new information concerning Code, whose powers surpass Jigen. As that happens, something appears before Code, who has been keeping watch over the immature Ten-Tailed Beast in Kara’s possession!

Those with a Karma gradually lose control of their minds and bodies as they undergo Otsutsukification. Naruto convenes a Five Kage Summit to discuss what they should do about Boruto’s condition, as well as Cord, one of the leaders of Kara.

Naruto, proposes that the Chunin Exam be held to raise morale after Isshiki’s attack. Everyone is fired up for the exam, eager to show off the results of their training and experience they’ve gained from missions.

The final round of the Chunin Exam is announced. Many of Boruto’s classmates who didn’t advance to the final round of the last exam have made it this time. Also, the rules of the exam have changed: the use of Scientific Ninja Tools of your own creation is now allowed!

The final exam has finally begun. The first match of the individual competition in the form of a real match is the VS Houki.　The twenty-fifth team of Houki and, unusually among their peers, has been involved in the mission of the "Anbu" until now. So, while we don't know what he's up to, Inojin uses his signature technique "Choju Giga" from the very beginning to hunt down Houki. However, as Houki was waiting for a chance, he suddenly lost sight of his opponent's location and the game was reversed. Who will win ......?

In this game, you'll have the chance to take the final exam, but you'll have to be careful not to get caught.

The final test, this time it's Iwabe vs Wasabi.　The two have a strong competitive spirit and usually clash with each other, but for some reason Iwabae is bewildered by Wasabi's unusual lack of energy. Wasabi, in fact, is feeling overwhelmed by the pressure of representing the hitherto unproven Izuno clan. Iwabeye is angry at Wasabi for setting her own limits on her ability and giving up. ......?　Who will be the victor in this match?

The match between Sarada and Cho-Cho begins. Kawaki has been invited by Naruto to observe, as well as Shinki and others who have come from the Hidden Sand Village. Who will emerge victorious in a battle between best friends?!

One after another, the winners of the finals are being decided. Only a few matches remain, but Boruto and Mitsuki still have not appeared at the venue. Sarada worries that at this rate, the duo will be disqualified. Meanwhile, the next match is between Denki and Tsubaki.

Team 7, with Sarada as captain, are assigned a mission. Mirai, who was on a mission with Konohamaru, returns to the village critically injured. The mission was supposed to be simple, but Mirai reports that the situation has changed drastically. It’s decided that reinforcements will be sent and Team 7 volunteers to go.

In order for Kawaki to become a genin, it’s decided that he can take a special test that differs from the one held at the Ninja Academy. A D-rank mission is deemed to be equivalent, so Kawaki is assigned as an additional member. However, he is difficult to work with, ignores the need for teamwork, and acts on his own—giving his teammates a hard time while disrupting the mission!

Kawaki starts to believe that being a genin is not for him. The Seventh Hokage gives him a last shot and assigns him to join Shikadai and Cho-Cho on a mission to protect Mozuku, from the Land of Calm Seas, and escort him back to his homeland. Will Kawaki be able to cooperate with his comrades and fulfill the mission this time? Meanwhile, Team 7 is on another mission and they pass a group who seem to be ninja in disguise…

Cho-Cho is injured in an attack by a mysterious ninja and the item that Mozuku had been holding is stolen. Captain Shikadai realizes that this was no ordinary guard mission, but one that makes them the targets of other ninja. He immediately decides to turn back toward home. But Kawaki feels for Mozuku, who was entrusted with the item that would save his people, so he ignores Shikadai's orders and pursues the ninja along with Mozuku. All alone, Kawaki faces a powerful enemy who uses a strange jutsu. Will he be able to protect Mozuku and safely return him to the Land of Calm Seas?

Traveling merchants have been attacked by vicious robbers. Wasabi, Namida, and Tsubaki of Team 15 are sent to the site of the incident to investigate. Tsubaki finds a clue that seems to point to samurai from her homeland, the Land of Iron. Furthermore, the clue belongs to a certain person that makes Tsubaki tremble in fear. That person is someone that she respected long ago, a fellow apprentice with whom she trained and honed her swordsmanship with—someone with whom Tsubaki shares a certain fate!