Dragonball GT starts about 10 years after Dragonball Z. Goten and Trunks have grown up, and Gohan and Videl's daughter Pan is a teenager. Near the beginning of the series, Pilaf (from Dragonball) gathers the dragonballs and when Gokou tries to prevent his wish, he wishes that Gokou become a kid again. That is the end of Pilaf.
Popo tells Gokou that there are dragonballs in space, called the Black Star Dragonballs, and Gokou goes with Trunks to find them, and wish himself back to an adult. For some reason, the earth will also explode if they don't succeed in gathering the dragonballs within one year. Pan stows away aboard their space ship when they leave.

While onboard, Pan damages an enigine. This causes the ship to crash land on a variety of planets, and during these crashes the heroes collect dragonballs, fight, and meet some local people. On one of their stops, their dragonball radar locator gets eaten by a robot named Gill, who they take with on their journey. Gill leads them to his creator, Dr. Myuu, who is in the business of making evil robots. One of his creations, Baby, is the centerpiece of this series.

Baby is actually a Tsufuru-jin, saved from space by Dr. Myuu after the Saiyans destroyed his home planet, long ago. Baby has the ability to take over people's bodies and absorb their power, similar to previous villains. He takes over Dr. Myuu, then sets out for revenge against Saiyans.

The heroes return to earth with the Black Star Dragonballs, and unfortunately they lead Baby back with them. Baby takes over Trunks, Gohan, and Goten, and can even control them without being in their body by planting a small controller inside of them. Baby takes over Vegeta's body, creating Vegeta-bebi, and is happy with the result. He turns everyone else on earth into zombies using his small control devices except for Mr. Satan, Gokou, Pan, Boo, and Ubuu. He also takes the Black Star Dragonballs from Popo, who was keeping them for Gokou, and wishes for a new home planet.

Now the fight against Vegeta-bebi begins. Ubuu fights him, then Boo fights him. Then Boo and Ubuu fuse together, and still can't defeat him. Young Gokou fights Vegeta-bebi, but is also defeated, even at Super Saiyan level 3. Kaiou-shin whisks Gokou away do his planet before Gokou can be killed, and helps him to regrow his tail.

Gokou begins to fight Baby again on Baby's new home planet, but is still defeated, until he sees the earth in the sky, which turns him into his beast, or Oozaru, mode. Gokou thrashes everything in sight before gaining control and reaching a higher level of power known as Super Gokou 4. He is about to win when Bulma (who is a zombie) creates a magnifying glass to amplify the earth's glow and allow Vegeta-bebi to also enter Oozaru mode.

While they fight, Kaiou-shin discovers that Chou-shi water removes the zombie contoller from people and sets about restoring earth's inhabitants. Gohan, Goten, and Trunks all donate some energy to Super Gokou 4, and he is finally able to kill Baby.

After the battle, everyone but Piccolo is brought to Baby's new planet, and the earth explodes because the Black Star Dragonballs weren't used to save it. The Namek dragonballs restore the earth, but Piccolo doesn't come back to life.