In the future, an older Boruto fights Kawaki in a destroyed Konohagakure, and argue about the end of the age of shinobi. Both activate seal-like powers, Boruto activates a dōjutsu in his right eye, and both resume their fight.

In the present, Boruto and Shikadai run through Konoha. In the Hokage's office, Naruto and Shikamaru go to his office, where Naruto bemoans the amount paperwork due will keep him from going home that night.

On top of a train, Boruto celebrates being able to buy a limited edition chilli burger. As they eat the two comment on the village's modernisation, and Shikadai scoffs at the prospect of having to attend the Academy. Shikadai tells Boruto to behave at the Entrance Ceremony, since it also reflects on him. Boruto leaps off the train after being spotted, and spots Denki being picked on. Boruto attacks the bullies with shadow clones, and makes a run with him as more arrive. Though they escape, Denki is worried the bullies will come after him harder the next day and comments on Boruto's ninjutsu. He learns Boruto is set to start at the Academy the following day, like himself. Denki's father wants him to learn ninjutsu as well as academics if he wants to inherit his company, crediting his achievements in the last war for the success of his company. Boruto tells Denki to tell his father about his wishes. The two talk more about their fathers, and Boruto realises he's late for dinner, fearing his mother's punishment.

When Boruto gets home, he argues with his mother about his father's absence during dinner, while Denki confronts his father, who says he'll allow Denki to study whatever he wants if he proves he is strong. Denki is bitten and influenced by a chakra snake.

The next day, Boruto is late for the Entrance Ceremony. Intending to take the train, he spots Denki and perceives a shadow over him, not noticing his own right eye changing. Denki lures his bullies into an old, malfunctioning train. Denki shows his bullies he put that train on a collision course with another defective train. Having followed Denki, Boruto shows himself and tells Denki to stop, and again perceives the influence on him. Boruto's words loosen the influence on Denki, and when he needs his help in changing the tracks, the influence on Denki is broken, allowing him to help. The two are able to change the tracks, and the bullies hold on to them when they almost fall off the train. They disconnect a wagon with the bullies, allowing them to stop safely. Still wanting to get to the Academy, they derail the train and crash it into the Hokage Rock. They arrive at the Academy during roll call, but damage Naruto's stone face. The other students are cleared out, while Konohamaru gets Boruto. At the end of the day, Naruto receives word that Boruto took the blame, but Denki's father offers to pay for the damages. After his suspension is up, Boruto heads to the academy and sees Denki, who got into the ninjutsu program, hoping to one day merge ninjutsu with science. Boruto decides against asking Denki about the shadow that had come over him. Looking up at his stone face, he vow to walk his own path in life.