This series starts off as Dr. Gero plots his revenge. He starts off by creating Android #19 to destroy Goku. Dr. Gero later asks Android #19 to make him into a robot like him so that he would be stronger, and he becomes Android #20! The Z Warriors meet with Androids #19 and #20 and fight. Goku leaves the battle because the heart disease that Trunks told him about starts to hit him. Vegeta faces Android #19 and, to everyone's astonishment, turns Super Saiyan. Dr. Gero's plot fails and Android #19 is destroyed. Dr. Gero is also destroyed to pieces, but he programmed himself to auto-repair and survives.

Android #20 then works on developing a better android model. Meanwhile, he unleashes two of his other creations, Android #17 and Android #18. Androids #17 and #18 get annoyed of Dr. Gero. As a result, they kill Dr. Gero. But, the doctor had just finished creating Android #21, who is still developing in a giant test tube. Before he dies, he issues the final command to his new android to feast on the rebellious androids. Android #17 and Android #18 leave the lab and unleash Android #16. But as it turns out, Android #16 is a peaceful android. As time passes, the Z Warriors become aware of the new androids as they battle again and again but always reach a stalemate. However, the Z Warriors are still not match for the androids because the androids are robots, and therefore do not tire in a long battle while the Z Warriors eventually run out of energy. The Saiyans do not continue to fight the androids. Instead, they train in a chamber to get stronger. Meanwhile, Piccolo fuses with Kami, his half father, to become stronger. Dende, a Namek child, replaces Kami as guardian of the dragonballs.

Androids #16, #17, and #18 go to seek Goku to destroy him. Piccolo finds the androids first and begins to fight them. Back in Dr. Gero's lab, Cell has finished developing and breaks out of the giant "test tube", promising to fulfill his creator's wish.

Cell flies to find Androids #17 and #18. On his way devours the souls of the unlucky civilians he passes to become stronger. Finally, he meets with the other androids. To our heroes' surprise, they learn that Androids #17 and #18 know nothing about Cell. Cell and Android #17 threaten to kill each other. Android #17 heads out to fight him. But, he does not stand up to Cell and is easily defeated. This is when our heroes learn the great powers of Cell. Android #18 is now worried, but Android #16 flies out to fight Cell. To everybody's amazement, Android #16 is able to stand up to Cell. However, he is still destroyed. Cell now heads for his goal and devours Android #17 with his tail. Cell now changes into Cell-form 2. With the power of Android #17 combined to his, he becomes stronger than ever. Then, he heads over to devour Android #18. Android #18 tries to escape, but she is still eventually devoured. Cell now changes into Cell form 3, and becomes "Perfect Cell", after devouring the souls of so many people, is no longer an android and becomes organic.

After Cell is gone, Bulma collects the body parts of Android #16 and repairs him. But, he is re-programmed to fight on the Z Warriors' side. Our heroes now head out to fight Cell. But, Android #16 is once again destroyed. Cell grows strong enough and reproduces. From his body came 7 Cell Juniors, young, blue duplicates of Cell. After a few more battles, Gohan, now a teenager, watches Cell crush #16 and Gohan reaches Super Saiyan level 2. He then destroys all the Cell Juniors. In one of the battles that follows, Cell is kicked and Android #18 is spit back out. Cell turns back into form 2 and is defeated. But, he activates his self destruction mode so that when he dies, the world will blow up with him. To save the Earth, Goku teleports Cell out of Earth and into Kai’s planet, where Cell blows up. Thus, Goku, King Kai, Kai’s gorilla, and Kai’s grasshopper die as well.

The Z Warriors mourn the loss of Goku, but at the same time they cheer at the victory over Cell. Unexpectedly, a fireball flies out of nowhere and pierces through Trunks. Upon Trunks' death, Cell, in form 3, appears. He tells that when he blew up, a brain cell survived. From the cell, other cells multiplied and he was once again formed. Cell happily laughs as he tells that he is amazed he is able to rebuild himself into form 3! Then, Cell threatens to destroy the earth. Vegeta tries to take on Cell, but is knocked down in one blow. Cell fires a shot at him that would have killed him, but Gohan rushes over and takes the blow, injuring his arm. For the first time ever, Vegeta apologizes. Now it was up to Gohan to try to save Earth. With one arm, Gohan prepares a Kamehameha. He fires at Cell and Cell fires back. A stalemate is meant, but with Kai’s help, Goku is able to talk to Gohan and encourages him. Meanwhile, Krillin protects the unconscious Android #18 and Yamcha, Tenshin-han, Piccolo and Vegeta attack Cell in hope that this will Gohan distract Cell. Krillin eventually joins them. With the help of the now dead Kai, Goku, also dead, is able to communicate with Gohan and tells him to use all his power to defeat Cell. Gohan overpowers Cell and Cell is disintegrated by Gohan's Kamehameha. But, Mr. Satan takes credit for Cell's death and lies to the reporters.

At the end, the warriors gather the dragonballs to bring those killed by Cell back to life. However, Goku is still dead because he was already brought back to life once and cannot come back again, but tells that he is okay and is now with Kai. Android #18 awakens and flees. However, everybody learns here that Krillin has developed a crush on Android #18!