The movie starts off with Baby's defeat at Super Saiyan 4 Goku's hands. The scene then fastens 100 years into the future. All of the Z Fighters have died of natural causes, except Pan, who is old. She has a grandson named Goku Jr., who resembles her grandfather Goku but lacks the latter's courage and fighting spirit. Pan takes Goku Jr. to the cemetery to pay their respects to her grandfather. She then tries to get him to train, but he has no confidence and skills in anything. At school, he is bullied by Puck, a senior classmate, and his gang, who take his favorite pen. Pan is angry that Goku didn't fight back and is so carefree. This causes her blood pressure to rise and she faints, and is hospitalized.
Back home, Goku hopes his grandma won't die, but then remembers that he could retrieve a Dragon Ball to make Pan better again. The next morning, he sets out for the Dragon Ball and encounters Puck and his gang along the way. One of Puck's friends asks where Goku is headed, and he tells them Mount Paozu. Goku faces put-downs from the gang, telling him he can't go there because there are monsters of all sorts and that he is a coward. The continued put-downs eventually make him angry, and he tells them to get out of his way. He walks by the gang and proceeds down the road to Mount Paozu. After following the road for hours, he rests for a moment. A truck passes by, and the truck driver offers him a ride. Goku accepts the driver's offer. After driving for a while, the truck driver pulls over and tells Goku to relieve himself because the trip will be long. While Goku is doing his business, the driver empties his oversized book bag (which is full of food), and throws the bag onto Goku, and speeds off. Goku, surprised, shrugs it off and continues the long journey to Mount Paozu. He meets Puck yet again at a roadside grocery store, who tells him that he became bored and thought it was interesting if he went to Mount Paozu with him, admitting that it would be fun to see a big monster eat Goku.
To acquire supplies for the long journey, Puck steals a cart full of food with Goku and escapes the grocery store just in time. After encountering obstacles along the way, such as a pack of wolves and a "nice" lady who turns out to be a witch, Goku and Puck finally make it to a long rope-and-wood bridge, which looks dangerously unstable. Puck crosses the bridge first with ease, telling Goku that it seems okay to cross it. Goku crosses the bridge nervously, and a gust of wind distracts him, which makes him stumble. Because Goku stumbled, along with the force of the wind, the bridge rocks back and forth, which was enough to break a rope. With one rope cut, the bridge becomes extremely unstable, and Puck had to rescue Goku before he falls. Puck struggles to save Goku, who is dangling on only one rope above a deep trench. Another rope is broken, and the bridge collapses, causing Puck to fall into the trench. Luckily, Goku was still dangling on half of the bridge, which is still attached to the other side of the trench. Goku climbs out, and with nothing to do to save Puck, continues his journey alone.
After traveling another great distance, Goku runs into a purple pig like demon, with the ability to manipulate his forearms into weapons. A grizzly bear, thankful to Goku for helping her cub earlier, attacks the demon trying to distract it so Goku and the cub could escape. Goku becomes enraged, and transforms into a Super Saiyan. He easily dismisses the demon, and soon after passes out. When he comes to, he has no memory of the transformation. Goku arrives to the summit of Mount Paozu, where he finds the old house which Grandpa Son Gohan harbored his ancestor in. He goes inside the old, dusty house, and finds the four-star Dragon Ball in the same place Goku kept it when it was first seen in the first episode of Dragon Ball. Goku takes it and, thinking that you can have one ball to grant the wish, tries to summon Shenron. When nothing happens, Goku becomes aggravated and shouts at the Dragon Ball as if there is someone in there. Again, when nothing happens, Goku throws the ball away, and starts yelling, telling himself that he was foolish to believe such a fairy tale about the Dragon Balls. Apparently, the Dragon Ball rolled to the feet of Goku Jr.'s ancestor, Son Goku himself.
Goku explains to his descendant that he has to collect all seven to get his wish. Goku Jr. gets on his feet, wipes his tears, and turns to his ancestor, stunned to see him. He asks him who he is, and Goku explains that he is his "great-great-grandfather." Confused about how many "greats" that would be, he tells Goku Jr. that he could just call him "Grandpa Goku" in short. Goku explains to Goku Jr. that he is strong and brave, because of his lineage. Out of the blue, a helicopter descends upon the ancient lawn of Grandpa Gohan's property, and reveals that Pan and Puck are inside it. Goku Jr. becomes excited to see everyone alive and well, exclaiming that the Dragon Ball granted his wish. He turns to where Grandpa Goku stood, and is stunned to see that he is nowhere to be seen, but Goku Jr. could hear his voice. Grandpa Goku tells him that it was actually his bravery that restored his grandma's life, including Puck's.
In a final farewell, Grandpa Goku wishes Goku Jr. good luck. Goku Jr. boards the helicopter with newfound strength, courage, and bravery with the four-star Dragon Ball in his hand. The Dragon Ball will be a keepsake for Goku Jr. to remind him of Grandpa Goku, just like how Grandpa Goku kept the Dragon Ball as a keepsake of Grandpa Gohan. Later, he reappears at the World Martial Arts Tournament where Goku is at the finals. He is apparently going to fight Vegeta's descendent.