After meeting up with Master Roshi, who makes it his business to bump into every fine woman in site, and his granddaughter Pan, who demonstrates her strength by kicking some bank robbers' asses, Goku returns home. Up on arrival, Chi-Chi is distraught that Goku is now so much younger than she is (she thinks it's some sort of conspiracy against her). It's at this point that Kaio-sama interrupts Goku and friends with some alarming news. Apparently, Kaio-sama had forgotten to inform Goku that the Ultimate Dragon Balls had put a great deal of strain on the Earth. If the balls are not returned to Earth within one year, Earth will be destroyed.

At this point, it is decided to launch a mission into space in an effort to collect the Dragon Balls. Hearing this, Vegeta knows of two saiyans who have been slacking off as of late. He collects Trunks and Goten and informs them both they will be going with Goku to collect the Dragon Balls. However, as Goten delays the launch by talking to one of his girlfriends, Pan sneaks on board and accidentally launches the spaceship. And so begins the search for the seven Ultimate Dragon Balls.

The space capsule crashes into many planets. In these planets, our heroes acquire the Dragon balls and meet a cast of minor characters. (It was these boring scenes that made people hate Dragon ball GT at first.) During these scenes, Goku and Trunks enter their Super Saiyan form for the first time in Dragon Ball GT to battle the minor villains. Pan also fights, but spends most of her time watching the Super Saiyans in amazement. In addition, our heroes meet Gill, a little robot who swallowed the Dragon Ball radar. As a result, our heroes take him on their journey.

Our heroes land on Dr. Myuu's planet. Dr. Myuu is an evil scientist who creates a bunch of cyborgs and robots. Gill is one of his creations. Trunks is kidnapped. Pan tries to rescue Trunks while Goku fights Ruudo, a creation of Dr. Myuu. Ruudo is killed. Gill helps Trunks and Pan escape and our crew returns to space.

One of Dr. Myuu's project is Baby. Baby is really the only surviving Tsufuru-jin. Planet Plant, his native planet, was destroyed by the Saiyans back when the Saiyans worked as mercenaries for Frieza. As the only survivor, Baby wants revenge on all Saiyans, innocent or guilty. Dr. Myuu found Baby in space and saved him. Baby has the power to take over bodies and acquire his victims' power. Baby takes over Dr. Myuu's body and kills him in the betrayal.

Goku, Trunks, Pan, and Gill finally return to Earth with all seven Black Star Dragon Balls. Goku takes them to Popo to secure them for later use. However, Baby also lands on Earth. Slowly, he takes over the bodies of Trunks, Gohan, and Goten. Even when he leaves their bodies, an egg is left in their brain. This egg makes its victim a zombie of Baby. (When Gohan was Gohan-Baby, he fought and injured Piccolo with a fireball.) Baby finally finds a body that satisfies him- Vegeta's! Vegeta's body is taken over and Vegeta-Baby is formed! Soon, everyone on Earth become zombies of Baby except Sataan, Pan, Buu, Ubuu, and Goku. Popo, also a victim of Baby, uses the Black Star Dragon Balls to create another Planet Plant for Baby. (By this time, Dragon Ball GT began to get interesting and unsatisfied fans began to take up interest in this sequel series to Dragon Ball Z.) Ubuu faces Vegeta-Baby and is defeated. Fat Buu joins the battle and is killed. Buu's body is near Ubuu and his spirit enters Ubuu. The two fuse and Ubuu learns that he and Buu were originally one. However, even with this fusion, Ubuu is no match for Vegeta-Baby.

Goku faces Vegeta-Baby. Vegeta-Baby is stronger and easily defeats the young Goku. Goku powers up to Super Saiyan level 3, but is still defeated; Vegeta-Baby can also power up to level 3. Pan hides in the background and watches the fight. The defeated Goku is pulled out of the fight by Kaiou-shin. On Kaiou-shin's planet, the Kaiou-shin inhabitant substances are creating a formula that will make Goku's tail grow back. (The tail is the main source of power for a Saiyan.) Goku's tail is only partially grown. Kaiou-shin pulls it to make it reach normal length.

Goku returns to planet Plant to face Vegeta-Baby. After getting beaten by Vegeta-Baby again, Goku lies on the ground and stares at the Earth. The "full-Earth" acts as a full-moon. As a result, Goku reaches Oozaru stage and becomes a giant golden ape. (The ape is gold instead of brown because it was the Earth that caused the transformation instead of the moon). Goku is a lot stronger, but is unable to control his body in Oozaru stage and trashes everything in sight. Another change occurs. Goku acquires control over his body and enters another stage beyond Oozaru. He powers up and becomes Super Goku 4. The tide of the battle is turned and Vegeta-Baby is losing. The zombie Bulma creates a special magnifying glass for her husband. It magnifies the rays of the full-Earth and Vegeta-Baby enters Oozaru stage.

Goku gets defeated once again. Meanwhile, Kaiou-shin resolves that Chou-sui water could cleanse people from Baby's control. He goes to Sky Palace to get the Chou-sui water. Dende and Popo are cleansed in the struggle against Kaiou-shin. This water is spread to everyone. Gohan, Goten, Trunks, (now free from Baby's control) and Pan surround Goku and form a circle. Their energy is donated to Goku. Goku and Vegeta-Baby face each other again. Goku does a Kamehameha fireball and defeats Vegeta-Baby. Baby leaves Vegeta's body and runs to a space capsule to escape, but is killed.

The Earth is about to explode because the Black Star Dragon Balls weren't used to wish for the Earth's stability. Our heroes fly all the inhabitants to planet Plant. Piccolo decides to stay on Earth to die with it because he loved it so much. (He is still injured from the blast from Gohan-Baby.) The Earth explodes, and Piccolo goes with it. At The Namek Dragon Balls are gathered and the Earth is restored from the wish, but Piccolo is still dead. However, one thing is learned- Goku reached a new stage as Super Saiyan...