It is now 3 years after the arrival of the mysterious boy. He had told Goku that they were supposed to train for the arrival of two strong beings, androids, created by Dr. Gero. They did as the mysterious boy told them, they trained hard for three years. They waited for the arrival of the two androids in the place that they were said to be, and there they meet Android #19 and Android #20. 19 is the first of a series of creations to destroy Goku. Along with the scheme, Dr. Gero requests 19 to make him (Dr. Gero) into a cyborg so that he would become stronger, and so Dr. Gero is transformed to 20. The Z Warriors meet with 19 and 20 and the two sides engage in battle. Goku leaves the battle because of his heart disease and leaves the battle to Vegeta (who has trained in to a Super Saiyan).
The android is destroyed and Dr. Gero is shattered. Despite the grave defeat, Dr. Gero's cybernetic programming enables him to self-repair, so that he may live to fight again. Future Trunks comes back to help out. There is a big dispute about two different futures. Trunks never saw 19 and 20 in his future. Meanwhile, 20 escapes to his lab.
20 then works on developing a better android model. Meanwhile, he unleashes two of his other creations, Android #17 and Android #18. 17 and 18 get annoyed of Dr. Gero. As a result, 17 kills 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. 17 and 18 leave the lab and unleash Android #16. But as it turns out, 16 is a peaceful android. (This can be shown through his love towards the wild animals.) 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. Goku who suffered the heart disease in one battle retreats. Trunks, who was sent back in time by future Bulma with medicine to heal Goku's heart so that Goku would live to kill the androids and thus change the future, gives Goku the medicine. Goku is saved, but the Saiyans still do not continue to fight the androids. 16, 17, and 18 go to seek Goku to destroy him. Cell has finished developing and breaks out of the giant "test tube", promising to fulfill his creator's wish. He then goes to find 17 and 18 to become complete.
Vegeta and Future Trunks train in the Time Room and both become Ascended Saiyans. After them, Goku and Gohan go in. Piccolo finds the androids first and begins to fight them. Cell flies to find 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 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, 16 is able to stand up to Cell. However, he is still destroyed. Cell now heads for his goal and devours 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. Vegeta, who is a true Saiyan seeking the best of fights, lets Cell absorb 18. Cell then heads over to devour 18. 18 tries to escape, but she is still eventually absorbed. 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.
In the Time Room, Gohan becomes a Super Saiyan. Vegeta is no match for Cell and gets beat up. Trunks then unleashes his real powers to fight Cell. He fights Cell, but the android is far too strong. Cell then tells him that he’s planning a Martial Arts Tournament where all the Z Fighters will fight one-on-one with him. After Cell is gone, 16 is fixed and reprogrammed by Dr. Briefs (Bulma’s dad) to fight on the good side. Our heroes now head out to fight Cell.
Mr. Satan attempts to fight Cell, claiming to be the strongest man in the world, but does no damage to Cell. It is now Goku's turn to do battle with Cell. A battle that is so fast, that a regular person cannot see it with the naked eye. At first, the two just play around and give the other hopes, but later on, they fight for real and this proves to be a very hard battle. Goku fires a Kamehameha at Cell that blows away his head and arms. But Cell with Piccolo's power, is able to grow out a new one. After this things look bad for Goku, and so he gives up and tells his son, Gohan to fight instead. Gohan does as his father tells him, but is still not fighting with his maximum power.
Cell tries to make Gohan angry so he can release his powers by expelling from his body 7 Cell Juniors, miniature blue duplicates of Cell. These Cell Juniors are beating up all of Goku's friends while he is just watching everything. 16 tries to destroy Cell by self-destructing, but Bulma had taken away the bomb inside him and so Cell kills him. After he is dead his head is still able to talk. And so 16 asks Mr. Satan to throw his head towards Gohan so he can talk to him and so he does (this is the only real thing that Mr. Satan does in this tournament). When 16's head arrives at Gohan's feet, he talks to him and tells him that some people will never understand with words, and to let out all of his hidden powers. At this, Cell walks towards Gohan and steps on Android 16's head, which finally kills him. The death of 16 triggers his anger; an enraged teenage Gohan powers up and reaches Super Saiyan level 2. Gohan then destroys all the Cell Juniors and fights Cell easily, while not even Goku was able to keep up with them (The Cell JR’s.).
In a following battle, Cell is kicked and 18 is spit back out. (She is unconscious.) 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 King Kai's planet, where Cell blows up. Thus, Goku, Kai, Bubbles, and Gregory die as well.
The Z Warriors mourn the loss of Goku, but cheer at the victory over Cell at the same time. 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. Now it is up to Gohan to try to save our planet. With one arm (the other injured when he went to let a fireball meant for Vegeta hit him), Gohan prepares a fireball. He fires at Cell and Cell fires back. A stalemate is meant, but with King Kai's help, Goku is able to talk to Gohan and encourages him. Meanwhile, Krillin protects the unconscious 18; and Yamcha, Tien, and Vegeta attack Cell in hope that this will help Gohan, by distracting Cell. With the help of the now dead Kai, Goku, also dead, is able to communicate with Gohan and encourages him to use all his power to defeat Cell. Gohan overpowers Cell and Cell is disintegrated by Gohan's fireball. (But, Satan takes credit for Cell's death because of his 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 King Kai. 18 awakens and flees. However, everybody learns here that Krillin has developed a crush on 18! And there is peace on Earth.