Boruto nicknames the mysterious shadow “The Ghost” and is excited when he and his friends Shikadai and Mitsuki decide to solve the recent “Ghost Incidents.” Shino secretly lends Boruto a helping hand by giving their class an assignment to research different workplaces. Meanwhile, Sai, who once served in The Foundation of the ANBU Black Ops, makes a big discovery while investigating the same incident under orders from the Hokate.

Sarada agrees to return a teddy bear to a young patient at the hospital, but she forgets it on the train and goes into a panic. Despite having dismissed Boruto and the boys for sitting on the roof of the train, Sarada does exactly that in her desperate search for the toy. Cho-Cho happens to see Sarada and takes her to the station’s lost and found. Sarada retrieves her package and all is well, until…

Kagura unlocks the storeroom to let Shizuma take the Mist Blades. The New Seven Ninja Swordsmen begin an insurrection, the end goal being to turn their village back into the Blood Mist Village! News of the rebellion reaches Chojuro and Mei, the current and previous Mizukage. They are determined to execute the perpetrators, along with Kagura, who aided them. In order to change Chojuro's mind, Boruto makes an astonishing announcement.

Boruto and his classmates decide to go camping to try to catch the mysterious fish, the Eternal Carp, said to be unforgettably delicious. With graduation coming up this could be the last time the class does something together, so Boruto figures this is the perfect opportunity to catch one, but the fish proves to be very elusive.

The protest instigated by the Byakuya Gang against the Kaminarimon Company increases in intensity. The Leaf Shinobi, including the genin, are mobilized into action. The teams are assigned sections to keep watch over the protesters, and Team 10, made up of Shikadai, Inojin and Cho-Cho, takes up its position. But Shikadai notices something as he studies the position chart and rushes out on his own!

Team 7 enters the mine where the thieves had been hiding out, only to be attacked by a powerful, strange-looking White Zetsu. They find out the mine connects to a ruin belonging to Kaguya Otsutsuki. Team 7 decides to investigate and engage the White Zetsu. As they proceed deeper and deeper into the mine, they make a shocking discovery!

Naruto and Sasuke fight against Momoshiki Otsutsuki. Momoshiki gets defeated, but he's helped by Katasuke and his Scientific Ninja Tool. In the end, Boruto puts an end to Momoshiki's life. While dying, Momoshiki talks to Boruto and gives him the Karma Seal.

Boruto and Sarada sneak out of the village and head to Orochimaru's research lab to find clues about Mitsuki. After evading the ninja guarding the entrance, they get in. But what they observe at the facility and hear from Orochimaru makes Boruto realize that he never truly knew Mitsuki. Meanwhile, the village finds out that Boruto and Sarada have gone in search of Mitsuki, and Shikadai and his Team 10 are assigned a tracking mission to bring back them back.

Boruto and the others work together to obtain the Reverse Scale from Garaga. But the battle proves difficult, as Garaga has the power to sense the location of its enemies and turn them into stone. In the midst of battle, the team notices inconsistencies in Garaga's moves and comes up with a successful strategy to subdue him. Boruto is seized with a strange feeling and makes Garaga a proposition.

Kakou appears to take the former Tsuchikage back to the village, but Boruto confronts him and they fight. Kakou uses a rare and powerful Particle Style and pushes Boruto to the edge. Meanwhile, Shikadai manages to slip through the Akuta guards and heads for the Hidden Leaf to report on the situation in the Hidden Stone.

Ku appears once again to provoke and attack Boruto. Meanwhile, reevaluating his true will and intent, Ohnoki prepares for a fight to the death in order to stop Ku from doing any more harm.

Boruto and Sarada confirm Juugo’s appearance. However, Juugo is under the influence of a ‘Cursed Seal’, and has transformed into a ferocious monster. The ‘Cursed Seal’ is one of Orochimaru’s research materials. Even though it amplifies strength and stimulates that attack instincts of living beings, Juugo is someone who possessed that capability from birth. Juugo has lost control over himself and begins to attack, putting up a difficult fight against Boruto and his comrades. Even though he’ll be getting assistance from his friends, will they cause damage to Juugo somehow?!

Konohamaru tries to rescue Remon by checking up on Kankitsu, but he is caught and forcibly taken back to the Leaf Village. Boruto becomes suspicious when he sees Kankitsu alone and acting as if nothing has happened. He decides to investigate the situation, only to be shocked by the sight that unfolds before him! Meanwhile, Konohamaru is disciplined by the Hokage after receiving a complaint from Remon's village.

Due to Sasuke’s frequent absences from the village, he hasn’t had time to train Boruto. When Sasuke sends a message home, Boruto takes a peek at its contents and learns that Sasuke will be making a stop at a certain location in the Land of Wind. Determined to be trained by his mentor, he sneaks out of the village.

Urashiki is determined to get Shukaku's chakra and attacks ruthlessly. Boruto and Shinki form a united front and unleash each of their special jutsu. However, Urashiki proves to be a formidable opponent that neither Sasuke nor Gaara could defeat. Will Boruto and Shinki be able to find a way to counter him?

Boruto's quick thinking exposes Urashiki's trick that enables him to see into the future and they manage to inflict some damage. But before they can breathe a sigh of relief, Urashiki emerges again with an even stronger move, and they're back in the same predicament!

Boruto and the others can't help but feel that Kokuri is hiding something from them. Meanwhile, Tsukiyo, a lieutenant in the Mujina Gang who's also imprisoned in Hozuki Castle, schemes to get Kokuri transferred to Hozuki Castle II, where his henchmen lie in wait.

One rainy night, guided by Mikazuki the cat, Mitsuki rescues an injured man. Mysteriously, Mikazuki seems to take a liking to the man who says he’s come to visit his sister who works in the Leaf Village. Soon after, Team 7 is assigned to back up the Leaf Police Force on a security mission. Their client is a president of a company who is being targeted by a serial killer known as "The Rainy Day Killer.

Boruto and the team are determined to reach Asaka, the eldest brother of the Land of Silence Ninja, before Deepa does. They catch up to him, but Deepa arrives soon after and attacks ruthlessly. They try to counter, but nothing seems to work. In the midst of their panic, Victor appears!

Separated from Boruto and Sarada, Konohamaru battles Victor. But someone unexpected shows up to fight alongside him. Meanwhile, Boruto and Sarada are trying to defeat Deepa to even the score, but he still proves to be a formidable opponent despite all of their training.

The Yamanaka Clan, who have been tracking the village’s ingoing and outgoing traffic with their advanced sensory abilities, spearheads a plan to create a new sensory system and an operational test is conducted.

The showdown between Team 7 and Ao begins. Team 7 works together to bring Ao down with various attacks and jutsu, but he proves to be a difficult adversary due to his use of scientific ninja tools.

Delta uses her destructive beam that can neutralize any regenerative power. Undaunted, Naruto forcefully suppresses it with a Giant Rasengan. He then turns up the power of his jutsu and propels it towards Delta. Unfortunately, Delta has been fitted with Scientific Ninja Tools and is able to absorb any jutsu, no matter how powerful… What will be the outcome of this battle?!

Boro goes on a rampage and attempts to eliminate Boruto and the others. Boruto is beat down and falls unconscious. Then suddenly, his Karma activates and he becomes possessed by Momoshiki's spirit.

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.

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.

The Land of Water is taken over by pirates, and contact with Denki's Team 5 is lost. The new Team 7 joins up with a unit led by Kagura and sets out for Dotou Island to assist Team 5 and rescue the islanders. However, the unit is made up of Buntan, Hebiichigo, and Kyoho, who in the past had called themselves the “New Seven Ninja Swordsmen of the Mist.” Sarada and Mitsuki go ashore to scout the island while Boruto and the others stay back and watch the situation nearby.

As Boruto and the others ready their plan, they learn that one enemy unit is heading to the village ahead of the rest. Since they haven’t finished making preparations, the village will be in danger, so they hurry to evacuate everyone. Kagura worries that they won’t have enough people to fight. Just in case, he releases the curse placed on Buntan, Hebiichigo, and Kyoho, temporarily setting them free. Hesitantly, they agree to fight alongside Kagura and Boruto.

Araumi is furious about the loss of family members and many of his subordinates during the battles so far. He officially declares war against the Land of Water. Upon hearing this, Mizukage decides to fight him to the bitter end. As war between the Land of Water and the pirates becomes inevitable, Boruto is confused by Ikada’s decision to fight the Land of Water. He does everything he can to prevent any more casualties, and Sarada and Mitsuki assist him in his efforts.

Naruto has been asked to play himself in the popular Evil Jammer Kagemasa shinobi movie series. Konohamaru ends up playing the role in his place. Since this is his first movie appearance and the fact that he will be playing the Seventh Hokage, someone he looks up to, Konohamaru goes all out. However, he’s troubled when production doesn’t quite go as he expected. Upon hearing something from the assistant director, he proposes something to make the movie more enjoyable.

Kawaki has a hard time getting used to school life, but he succeeds in becoming friends with Princess Kae, the object of his guard mission. Meanwhile, Kae wants to get to know her classmates and invites them all to a tea party at her mansion. Since Kawaki has his mission and cannot let Kae out of his sight, he goes along. Despite feeling out of place at the party, Kawaki does his best to fit in, but then he senses something unusual…

Boruto accompanies Sasuke to a hawk trainer to obtain a messenger hawk.

There, Boruto and Sasuke hear about a person who sells rare animals and decide to investigate. Boruto then befriends a boy named Tsuzura Shitakiri. Because of his mother, Tsuzura doesn’t go to school and has given up on the things he really wants to do. His only friend is a hawk that is unable to fly due to an injury. He takes good care of this hawk in the hope that it can soar the skies once again.

Sasuke is attacked by Meno, the guardian of the Observatory, and then poisoned. Just when he thinks it’s all over, he is rescued by Sakura, who has infiltrated the Observatory as a doctor. She gets Sasuke reassigned to assist her, and they begin their undercover investigation. From the intel that Sakura brings, they learn that Ultra Particles were what cured the Sage of the Six Paths, but in order to find out where it is located, they need to obtain a document called the Map of the Heavens. They decide to search the Observatory’s library for it.

Amid a fierce battle, Kawaki’s fears come true, and Momoshiki takes control of Boruto. Kawaki watches as Boruto overwhelms Code as Momoshiki. Then Naruto arrives with Shikamaru. Kawaki is concerned for Naruto’s safety as one of Code’s targets, but despite his wishes, Naruto takes on Code as the Hokage. Unfortunately, Code takes Shikamaru hostage, and in his desire to settle his grudge, Momoshiki joins him. Naruto faces an extremely dangerous situation.