It's about three years after the Freeza series, and for the past three years, our heroes have all been training to fight the robots that Trunks had warned them about. Dr. Gero, whose Red Ribbon project was destroyed by Gokou way back in Dragonball, started designing a scheme for revenge three years ago. The project is taking too much of his time though, so he abandons working on it and just leaves the computer that it is developing on running.
On the day Trunks said he would return, Gokou and the other heroes, except the weak Chauzu, fly to the island where Trunks first appeared. There they find Bulma, holding a baby. She explains that the baby is hers and Vegeta's, and that his name is Trunks. The heroes then go to a nearby city in search of the androids. They find Android 19 and Android 20 when Yamcha is attacked by them. The androids and the heroes fly to Stone Mountain to fight.

Gokou and Android 19 fight first, and Gokou is losing even though he is at the Super Saiyan level because the Androids are able to absorb power, from people and from their attacks. Suddenly Gokou falls, stricken with his heart failure, and Android 19 starts to absorb all his energy. Then Vegeta comes, powers up to be a Super Saiyan, and beats Android 19. Android 20 flees the scene in fear.

Trunks arrives from the future, and tells the heroes that they are fighting the wrong androids. Android 19 and Android 20 don't cause trouble in Trunks' future; Android 17 and Android 18 do. Android 20, coinicidentally, is actually Dr. Gero - he had Android 19 turn him into an android. Trunks tells everyone that Android 17 and Android 18 are still being built, so they all head for Dr. Gero's lab to stop the androids from coming into being. Dr. Gero goes to his lab too, to stop them, and he arrives first.

When the heroes arrive, Android 17 and Android 18 have already been released. The androids kill Dr. Gero, then release another android, Android 16. Android 17 and 18 beat most of the heroes, but Android 16 doesn't help because it's supposed to only kill Gokou.

As the heroes recover and leave to look for the androids, they find a time machine - much like Trunks, but not his. According to Trunks, the future Bulma only makes one time machine, and there shouldn't be another one. When they go and look around the site, all they find is an empty, cracked shell.

Piccolo and Kami get together and they decide to fuse into one ultra powerful being. Piccolo thinks that this is the only way to defeat the androids, and Kami has been watching a strange creature absorb entire towns. Piccolo goes to the town where people have been vanishing and encounters Cell. The two fight for awhile, and then Piccolo asks Cell who he is and why he came. Cell explains that he is a creation of Dr. Gero's, part of the computer program that was left on. When Trunks returned from the past, having destroyed Andriod 17 and Android 18, Cell killed Trunks and used his time machine to return and save the androids. Cell wants to reach a 'perfect form' and Android 17 and Android 18 are vital to helping him acheive that. Now that he's rested, Piccolo resumes the fight and eventually Cell leaves.

Gokou recovers from his battle and teleports from Kame House to see Gohan, Vegeta, and Trunks. They all go to the Sky Palace and train in the Room Of Spirit And Time, where time passes so slowly that they can train for an entire year in just one day. The room has a maximum capacity of two, unfortunately, so Vegeta and Trunks enter first.

The androids go to Kame House and fight Piccolo, easily beating him, but then Cell comes. Cell beats Android 17, then gets injured by Android 16. Cell absorbs Android 17, becomes more powerful, and then destroys Android 16. Next he absorbs Android 18, and that brings him to his 'perfect form'.

By this time, Gokou, Gohan, Vegeta, and Trunks have all been able to spend some time training in the Room Of Spirit And Time, and they leave to help in the fighting. Bulma rebuilds the damaged Android 16 from scrap and reprograms him to help the heroes. Cell starts a tournament called the Cell Game. He will challenge all of earth's warriors, and if he beats them he gets to destroy the earth.

Gokou fights Cell first. The fight is very even, and they battle to a stalemate. Gokou then tells Gohan to take his place, give Cell a senzu bean out of fairness, and reassures everyone that Gohan becomes incredibly powerful when he gets angry. Gohan is beaten for awile but doesn't get angry enough to fight back. Cell becomes bored and destroys Android 16, then unleashs 7 minature Cell Juniors from his tail, which quickly overwhelm the spectators. Android 16's disembodied head lands near Mr. Satan, who is reporting the fight, and he convinces Mr. Satan to throw his head at Gohan. The head talks to Gohan, encouraging him to fight, but then cell crushes Android 16's head. This finally sets off Gohan, and he goes into Super Saiyan level 2, even more powerful than the regular Super Saiyan. Gohan really takes it to Cell, hitting him so hard that Android 18 pops out and Cell degenerates from his perfect form. Since Cell can't win, he activates his self-destruct sequence to destroy earth. Thinking quickly, Gokou teleports Cell to Kaiou's planet, saving the earth but killing himself and Kaiou.

Cell regenerates in his perfect form, saying that one of his brain cells was left behind and allowed him to reform. Vegeta blasts at him with numerous fireballs but does no damage. Cell quickly beats Vegeta, and Gohan has to take a fireball from Cell to save the helpless Vegeta. Then Gohan and Cell start shooting back and forth, their fireballs destroying each other in an endurance match. As Gokou yells words of encouragement to his son from beyond the grave, through the power of Kaiou, Vegeta fires a blast at Cell from above. This momentarily distracts Cell, and Gohan unleashes a flurry of the most powerful fireballs he can muster, utterly destroying Cell. After the heroes leave, the nearby Mr. Satan takes credit for destroying Cell and declares himself the strongest man in the universe.

The heroes go to Sky Palace. Krillin convinces them not to kill Android 18, then they gather the dragonballs. They wish to remove the bombs from the androids, and revive everyone killed by Cell. Unfortunately, Gokou remains dead.