In order to bring #18 and Krillin back to life, the Dragon Balls were gathered When Shenlong is summoned, something goes wrong. Shenlong appears, but he looks a bit different and laughs wickedly, he is evil. Our heroes learn that the Dragon Balls have cracked due to negative energy that stored inside the balls when negative wishes were made. A cloud appears around the evil Shenlong, and it transforms into seven evil dragons, each of a Dragon Ball. The dragons fly off in different directions and wreck chaos. Each dragon has its own element. When it finds that element, it will take on its true form.

Goku and Pan fly off to fight these dragons. First, they encounter Ryan-Shenlong. Ryan-Shenlong tells that he was born when Bora was wished back to life. This dragon of the 2 star Dragon Ball is of water pollution. It was tricked into swimming in clean water. After it was weakened by this action, Goku and Pan attack and kill it. The 2 star Dragon Ball is restored.

Next, Goku and Pan follow the dragon radar's signal and encounter Uu-Shenlong. It was born in the 5 star Dragon Ball when Goku was wished back to life to fight Raditz. This dragon of electricity was weakened in rain and destroyed in its weakened state. The 5 star Dragon Ball is recovered.

Ryuu-Shenlong is the next to appear. This dragon was born when Oolong made the wish for women's underwear while fleeing from Pilaf. This dragon possesses the power of hurricanes. Goku learns of its weakness and attacks it on the head. Ryuu-Shenlong was easily defeated and the 6 star Dragon Ball was restored.

Following this, Goku and Pan fly to Chii-Shenlong, which was born in the 7 star Dragon Ball when all the people killed by Majin- Vegeta were wished back to life. Pan gets tricked and becomes trapped in the dragon's body. Goku rescues her and destroys Chii-Shenlong. Another Dragon Ball is recovered.

Suu-Shenlong is next for Goku and Pan to encounter. It was born when Piccolo was wished back to life. This dragon of the sun is associated with the 4 star Dragon Ball. It challenges Goku in a match and the two fight. All of a sudden, San-Shenlong, Suu-Shenlong's brother and of the 3 star Dragon Ball, appears. After getting mocked by his brother for losing honor in interfering with the match, the dragon of ice fights Goku anyway. It is slayed in battle, and Goku and Suu-Shenlong continue their match. Goku admires Suu-Shenlong's sense of honor. The match becomes interfered again when another third party kills Suu-Shenlong. This party is Ii-Shenlong, of the 1 star Dragon Ball. Goku defeats it in Super Goku 4 stage, but the dragon survived. It defeats Pan and steals all the restored Dragon Balls. Ii-Shenlong fuses with the balls and powers up. Super Goku 4 is no match for it in its fused state.

Bulma created a brute ray that allowed Vegeta to go Super level 4, and Super Vegeta 4 joins Goku in battle. The two are still no match for Ii-Shenlong. Another strategy is used: Super Goku 4 and Super Vegeta 4 fuse and become Super Gozita 4! Ii-Shenlong is kicked around and the Dragon Balls it fused with are restored, but the fusion of Super Gozita 4 wears off before Ii-Shenlong is killed. Ii-Shenlong fuses with the Dragon Balls once again, but Goku gets to the 4 star Dragon Ball before Ii-Shenlong can and swallows it so that the dragon can't fuse with it. Eventually, Goku spits the Dragon Balls back out and Ii-Shenlong absorbs it. Vegeta suggests to use fusion again, but Goku is too weak to go Super level 4. Therefore, he remains in his small size; he cannot fuse with Vegeta in this state due to size differences. Ii-Shenlong boasts to kill Goku and Vegeta. One last chance of hope remains. Goku begins to create a Genki-Dama. Everyone on Earth raises their hands to donate energy to Goku. Goku teleports to Kaiou and asks that the energy is not enough. The Kaious agree to help seek life forms across the galaxy to help donate energy to Goku. All the characters encountered in space in the Baby Series are shown again and they raise their hands. Goku's giant Genki-Dama is created and it destroys Ii-Shenlong.

All the Dragon Balls are restored to normal, but something is wrong. Shenlong appears without being summoned and tells that he will not make any more wishes because of all the trouble the Dragon Balls have caused. Goku convinces it to make the final wish of restoring all the civilians killed during the fights against the dragons. The wish is granted, and Goku is told to ride on Shenlong's back. Goku does so. Chi-Chi and her sons go home to prepare a big feast while awaiting Goku's return, unaware what's going on. Pan notices Goku's tattered clothes on the ground and asks if her grandpa is gone for good. Vegeta replies that he is. On the dragon's back, Goku visits the Z warriors. At the end, Goku lies down and the Dragon Balls are absorbed into Goku and Goku disappears. Shenlong coils up and flies at the camera. The screen turns white. As for the epilogue, 100 years have passed and Goku Jr. (Pan's grandson) is at the latest Boudaikai Tenkaichi tournament. He and Vegeta Jr. (Vegeta' descendant) are about to compete. The two boys to Super Saiyan level and fight. Pan is a spectator in the audience, and notices a familiar face in the crowd, it is adult Goku watching the fight at the other side of the stadium. Pan goes to him, but loses him in the crowd. Goku walks away, and clips of Dragon Ball Z-GT are shown.