The film begins in Metro City, a small city that floats above Earth, which is now covered in discarded robot parts. Toby Tenma finishes a physics pop quiz ahead of all his classmates and is free to leave, so he rewires Orrin (the family servant robot) who takes Toby to the Ministry of Science.
Toby's father, Dr. Tenma, is at the ministry, meeting with President Stone and Dr. Elefun. They have captured two cores of energy, a "positive" (good) core and a "negative" (evil) core. Toby is placed in a room where he is supposed to stay until the end of the demonstration, but he escapes and runs off to the demonstration room.
President Stone orders the Red Core to be placed into a robot called "The Peacekeeper" to power it. The Peacekeeper begins to malfunction and tries to attack the scientists, vaporizing Toby before the adults are able to deactivate the robot.
Soon after, Dr. Tenma is seen holding blueprints of a robot replica of Toby, in hopes of recreating his son. He takes hair from Toby's hat to access all his memories and place them in the robot. Dr. Elefun provides the Blue Core to power the very advanced Toby robot. The robot Toby comes to life, to the excitement of Dr. Tenma. Tenma then takes Toby home, at first excited to spend time with his son, but he quickly realizes the new Toby is not the same as the old Toby.
Dr. Tenma calls Dr. Elefun, fearing that he may have made a mistake. Dr. Elefun makes a point that Toby cannot be exactly duplicated. Dr. Tenma grieves over the fact that whenever he sees Toby, he is reminded that Toby is really gone and will never come back.
While in his room, Toby worries about his father, since he has never been that angry with him before. While Toby gets into a quarrel with cleaning robots outside his window, he discovers he can understand them but falls out the window only to discover that he can fly.
President Stone discovers Toby's energy signature and his blue core, and orders his troops to capture it. When Toby returns home he overhears his father talking with Elefun about deactivating Toby. Dr. Tenma reveals that Toby is only just a copy of the original Toby and that he no longer wants him since his face only reminds him of his real son and the pain of losing him. Devastated, Toby flies off but not before Elefun assures him that he has a place somewhere in the world.
Toby is ambushed by military drones and flying craft controlled by Stone's military. A barrage of missiles temporarily disables Toby, causing him to fall to the Earth's surface. Toby wakes up on the Earth's surface, covered in broken robots, where he meets a robot dog named Trashcan. Trashcan leads Toby to a trap where he is wrapped up and captured by a group of kids, but released when he appears to be a human. Toby is then abducted by the "Robot Liberation Front", who name him "Astro". They then warn him of Hamegg, who enslaves robots. Cora and the children break in to free Astro.
Tenma promises to President Stone that he will deactivate Astro when they capture him and give Stone the blue core for the Peacekeeper. Cora takes Astro to their home, filled with tons of children and the Fagin-like ringmaster Hamegg. However, Hamegg isn't as evil as he seems. Hamegg eagerly welcomes Astro into their family. Later that night, Hamegg talks with Astro and how he used to work in Metro City with Dr. Tenma, but was thrown away due to his "intimidating brilliance".
The next day while out searching for parts in Brazil, Trashcan tried to tell everyone else that Astro is a robot, but fails. (Trashcan eventually writes on the ground "He's A Robot" but then Zane comments "Makes me wish I knew how to read.") Astro finds a 100 year old robot named Zog. Using the power of his blue core, Astro revives Zog. They take him back to their home and fix him up for the robot games. But Astro is slightly upset when he discovers that it is a fight to the death. Before the games start, Hamegg electrifies Astro and reveals to everyone that he is a robot. So, Hamegg puts him in the games. At Yankee Stadium, Astro easily clears all the robots but is put up against Zog, who refuses to fight Astro. Hamegg, forcibly tries to get Astro to fight, but Zog attacks him (being over 100 years old, the rules of robots not being allowed to harm humans doesn't apply to him, since it has been the rule for 50 years). Astro then stops Zog, leaving Hamegg to wonder what kind of robot he really is. Just then the military arrives and Zog tries to defend Astro, but Astro stops Zog and goes with the military. Astro believes he needs he must fulfill his destiny, whatever it is.
Stone mockingly offers the captive Astro a "drink" of machine oil.
Astro is taken back to the lab he was made in and Dr. Elefun tells him that he is wonderful and none of this is his fault, but Astro believes that it is hard to fit in and that perhaps this is his destiny. Dr. Tenma takes out the blue core and apologizes to Astro, who says he shouldn't be sorry and apologizes for not being a better Toby. Astro then deactivates and dies. Dr. Tenma gives Stone the core, but repents of the evil he is doing and takes the core back, putting it in Astro. Astro wakes up wondering why Dr. Tenma has done that, but he replies that even though Astro is not Toby, he is still his son.
Astro escapes so Stone uses the red core to reactivate the Peacekeeper. The Peacekeeper absorbs Stone and heads to destroy Astro, with Stone's mind controlling it. With the Peacekeeper on the rampage, absorbing every weapon and structure it comes across, Astro flies into the city to protect it from the rampaging behemoth. Meanwhile, Cora and the others hijack Hamegg's car to head to Metro City and help Astro. In the resulting showdown, the city's power source is destroyed but Astro manages to hold it up and causing it to land unharmed before continuing battle with the Peacekeeper. He's captured by the Peacekeeper but when it tries to absorb him, it doesn't work. Dr. Tenma tells Astro that if the Blue Core and Red Core come together, Astro and the Peacekeeper will die. Knowing that the Peacekeeper must be stopped, even if it means sacrificing himself, Astro flies into the Peacekeeper's Red Core, resulting in a massive explosion that completely destroys the Peacekeeper, leaving Stone unharmed but arrested, and Astro dying since the blue core was drained in the explosion. However, because Zog was revived with the blue core, he is able to return some of the energy back to Astro, reactivating him.
Astro finds his place as a hero and everyone rejoices. Cora reunites with her parents. But before any celebrating can happen a large alien attacks the city and Astro, now at peace with his robotic nature and his destiny as a hero, immediately launches into action after reassuring his concerned father, "I was made ready!" The movie ends with Astro flying to fight the alien.
