The film begins in Metro City, a small city that floats above an Earth 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, demeterializing 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 quicly 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.

In a scene mirroring the taxi chase from The Fifth Element, Toby is ambushed by military drones. A barrage of missiles temporarily disables Toby, causing him to fall to the Earth's surface. Toby wakes up in the aftermath of a dystopian future (as fortold in Soylent Green) below Metro City filled with broken robots where he meets a robot dog, Trashcan. Trashcan leads Toby to a trap where he is wrapped up and captured by a group of kids, but released when they see he is not a robot. They introduce themselves to Toby, but before he can respond, a group of robots kidnap him. The group is the R.R.F (the Robot Revolutionary Front) who save robots and name Toby, Astro. They then warn him of Hamegg who enslaves robots. Just then, Cora busts in and takes Astro.

President Stone arrives to arrest Elefun and learns of what Dr. Tenma did with the blue core. He promises to 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 writes on the ground "He's A Robot" but then one of the kids 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). Just then the military arrives and Zog tries to defend Astro, but Astro stops Zog and goes with the military.

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. Dr. Tenma gives Stone the core, but betrays him and takes it 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, however, the Peacekeeper absorbs Stone and heads to destroy Astro. With the entire city cleared and the Peacekeeper souped up with a bunch of weapons. Meanwhile, Cora and the others hijack Hamegg's car to head to Metro City and help Astro. But when the Peacekeeper tries to absorb him, it doesn't work. Dr. Tenma says that if the blue core and red core come together, Astro and the Peacekeeper will die. Either way, Astro flies into the Peacekeeper and they explode, leaving Stone unharmed, but arrested and Astro deactivated since the blue core has been drained. However because Zog was revived with the blue core, he returns 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 and Astro, now at peace with his robotic nature, immediately launches into action after reassuring his concerned father, "I was made ready!"