The first Five Kage Summit since the attack by the Otsutsuki Clan is held in Hidden Leaf. The current Kage as well as their predecessors assemble, except the Third Tsuchikage, Ohnoki. Boruto and Team 7 have been assigned security duty, but Boruto gets bored and lets his guard down. Then by chance, they encounter Ohnoki.

The ninja assigned to the Hidden Leaf Gate are attacked, and Mitsuki disappears. Boruto and Sarada are unaware of this when their scheduled mission is suddenly canceled. Worried, the two start searching for their teammate. When they learn that all the jonin have been summoned by the Hokage, they set out to find out what's going on.

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.

Orochimaru tells Boruto and Sakura about the White Snake Sage who lives in Ryuchi Cave. On their way there, the two are confronted by Team 10, which is determined to take the two back to the village so that they are not labeled as "rogue" ninja. But there's no way Boruto or Sarada will oblige until they find out the truth from Mitsuki, so they are forced into confrontation using everything they've got!

Boruto and friends head for Ryuchi Cave in order to see the White Snake Sage. But it's not a simple task, since they have no clue where it is. They search for miles, becoming hungry and tired. They are near their limit when Ryuchi Cave suddenly appears before them along with mysterious women to guide them. They are told they must pass a series of tests in order to meet the White Snake Sage!

The White Snake Sage tells Boruto to bring back the "Reverse Scale" from Garaga, a troublesome snake. Boruto and his friends head deeper into Ryuchi Cave and are confronted by a giant serpent. It is Garaga, the very one they seek, but its sheer power has the gang backed into a corner. Meanwhile, Moegi reports that Mitsuki's disappearance might involve someone who has access to crucial village secrets.

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.

Mitsuki heads toward Kokuyou and Sekiei's homeland, the Land of Earth. Meanwhile, thanks to the power of the White Snake Sage, Boruto and the others learn that Mitsuki is with Hidden Stone Ninja, and they also head for the Land of Earth. Each side has their own agenda, but will they be able to meet up successfully?

Kokuyou confronts Boruto and the others. Kokuyou, whose only goal is to become strong, is so powerful that he's taken down the Leaf ninja pursuing Mitsuki. He easily drives Boruto and his team into a corner. Just then, backup appears. Boruto and his friends manage to overcome Kokuyou, and finally catch with up Mitsuki.

Instead of returning home with Boruto, Mitsuki stays with Kokuyou. During this time, Sekiei becomes sick and declines. To recover, Kokuyou returns to his comrades. During his absence, Sekiei asks Mitsuki to teach him what it means to be human. Meanwhile, the Fourth Tsuchikage Kurotsuchi, who had been visiting Ohnoki, her ailing grandfather, is attacked by mysterious assailants.

Boruto is injured, unconscious and unable to continue. Everyone thinks about returning to the Hidden Leaf. However, being close to the Land of Earth, a surprise attack is highly possible. As a precaution, Inojin and Cho-Cho set out on recon of the surrounding area.

Boruto and his friends decide to go the Hidden Stone Village to see the former Tsuchikage, Ohnoki. In case of an emergency, Inojin stays back with the young Akuta, who is attached to him. The team secretly enters the village determined to find Ohnoki, but they are unaware that they are being watched.

The team finds Ohnoki, but he flatly refuses to help. On top of which, they are attacked and separated. This leaves it up to each member to make it to the rendezvous point on their own. Meanwhile, Mitsuki is being shown around Kokuyou’s hideout.

Boruto and Ohnoki head to the rendezvous point, but they stumble into the Hidden Stone Shinobi Training Grounds, which are protected by a barrier. Ohnoki tells Boruto that the only way out of the Training Grounds is to find his heart of stone, something that can only be found once in a lifetime when a person comes to terms with their will.

In order to get out of the barrier, Boruto desperately searches for his heart of stone, but he has little success. Then he encounters Sekki, one of the Genbu Three that participated in the recent Chunin Exams. Sekki has also come to the training ground in order to find his heart of stone. Seeing their predicament, Ohnoki tries to help them.

Ohnoki takes Boruto to a special location to explain his vision of the future, formed after losing his grandchild, Kozuchi. Meanwhile, time is running out for Ku and his supporters. They rush to set their plan in motion—using force to subdue any who dissent, they attempt to take over the Hidden Stone Village.

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.

Boruto and Sarada are caught and taken back to the Hidden Stone headquarters along with Ohnoki. There, they find that Ku and his supporters have taken the village, and that things have changed drastically. Kokuyou and Kirara swoop down on Boruto and Sarada, but Shikadai comes to the rescue!

After Boruto and Sarada part ways with Shikadai and the others, Kirara appears and turns them into “dolls” that must obey her, ordering the two to kill each other. Meanwhile, thinking about Boruto’s words and how his village is becoming something different than what he envisioned, Ohnoki realizes that he’s made a mistake.

Sustaining great damage from Mitsuki’s attack, Ku flees the scene. Boruto and Sarada attempt to chase after him, but Kirara blocks their path! Meanwhile, Sekiei watches everything unfold. Shocked and confused by the actions of Mitsuki, Sekiei recklessly attacks him. Not wanting to fight, Mitsuki tries to stop him.

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 the other Leaf Genin return to the Hidden Leaf with Mitsuki. However, Mitsuki is detained and subjected to hours of interrogation. And since Boruto and the others have taken actions that would normally banish them from the village, it is decided that they will lose their genin qualification as punishment.