The ghost incident that threatened the Hidden Leaf Village is over, and now Boruto is unable to awaken the mysterious power he used. Things return to normal in the village and the Academy, but one thing still troubles Boruto and his classmates...

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…

Determined to rescue Sakura, Sarada pursues Shin with Sasuke, Naruto, and Cho-Cho. After brutal battles with Shin's clones along the way, Sarada is surprised to see the bond of trust between Sasuke and Sakura, who haven’t seen each other in years. But suddenly, Shin orders his children to kill the intruders. Since her parents share a bond of trust and love, will Sarada's journey to learn the secret of her birth reach a conclusion?

Boruto urges his friend Kagura to return with him, but Kagura rejects him and begins to attack. Although Boruto is desperate to save him, Kagura once again falls under a spell and is unable to defy Shizuma. Then someone steps in between the two as they battle. It's Mitsuki, and he has obtained intel about the rebellion. Just what is the intel, and can Boruto save his friend?

Boruto's the first to confront Kakashi in the exam. Despite a determined effort, he is immobilized and angered by Kakashi's severe criticism of his class. Shortly after, Boruto's classmates come by to assist and Boruto makes his escape. Although depressed by his own shortcomings, Boruto is able to overcome them and formulate a strategy, thanks to the encouragement of his friends.

Team 7's original mission evolves into a rescue operation after Kiri is kidnapped. The team must face a formidable genjutsu user as well as a skilled sword user. Following Konohamaru's orders, the team successfully rescues Kiri. But Konohamaru is captured and the trio must battle the enemy alone while protecting Kiri.

During the protests, the Byakuya Gang attacks Katasuke's research center, which has been developing new technology for Scientific Ninja Tools. Shikadai figures out what the Byakuya Gang's goal is and rushes after them in pursuit with Boruto close by. Even a weak "pawn" can become strong in one move—what are the two friends who bonded through shogi seeking?

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 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.

Jugo is suffering from the effects of the drug that activates the power of the cursed seals. Somehow or another. Boruto and Suigetsu want to try to save him, but they are rendered unable to move because of being injected with a tranquillizer. Meanwhile, it’s time for the migratory birds to set off.

Boruto and Shinki clash, and they ultimately end up going their separate ways. But an Otsutsuki puppet appears before Shinki. Just then, Boruto arrives with Shikadai and Temari, who were on their way to the Hidden Sand. Even with their help, the Otsutsuki puppet proves formidable. Meanwhile, Urashiki breaks through Gaara’s Sealing Jutsu and begins to move once again.

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!

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.

Koji Kashin retreats from battle after seeing that Boruto has a "Karma" mark on his hand. Shortly after, Team 7 discovers a battle site where a boy lies unconscious. Much to everyone's shock, the boy possesses the same mark as Boruto.

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?!

Boruto, Sarada, Mitsuki, and Kawaki arrive at the dimension that Naruto is trapped in, but Boro is there waiting for them. The four create a team with Sarada leading them to fight Boro, who uses a black mist to paralyze his enemies.

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.

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.