In the future, Metro City is a safe and prosperous municipality that floats in the sky above the surface of the planet below that's littered with old robots that have been discarded by the humans up above. The latest generation of those robots have been invented by Dr. Tenma (voice of NICOLAS CAGE) whose young son, Toby (voice of FREDDIE HIGHMORE), seems to have inherited his dad's smarts.
As head of the Ministry of Science working for President Stone (voice of DONALD SUTHERLAND), however, Tenma doesn't have much time for his son, instead allowing house robot Orrin (voice of EUGENE LEVY) to watch over the boy. When the scientist informs Toby that he's been called to work on the Peacekeeper project with his colleague, Dr. Elefun (voice of BILL NIGHY), the boy's interest is piqued.
Accordingly, he sneaks into the lab where he learns about the Blue Core, Elefun's peaceful power source discovered from outer space. But Stone wants the opposing and volatile Red Core inserted into the Peacekeeper robot, and the results are disastrous, with Toby ending up being accidentally killed in the resultant chaos.
Stricken with guilt, and using some of Toby's recovered DNA, Dr. Tenma creates a perfect robotic replica of Toby, but with advanced features, powered by the Blue Core, that should keep him safe. After a while, however, the scientist can't continue with the ruse and tells his son not only that he's a robot, but also that he no longer wants him. But President Stone does, or at least the Blue Core inside him. In the ensuing chase, the robot is knocked out and falls to the planet's surface.
There, he meets a bunch of orphans, including Cora (voice of KRISTEN BELL), Zane (voice of MOISES ARIAS) and Grace (voice of ELLE FANNING), who use an old robotic Trashcan, that believes it's a dog, as a lure to catch robots for Hamegg (voice of NATHAN LANE). He used to work for the Ministry of Science up on Metro City, but now runs a gladiator style contest down below for the amusement of humans. Since the Toby robot appears so human, however, the kids -- who are led to believe his name is Astro -- instantly befriend him, and they go about collecting Zog (voice of SAMUEL L. JACKSON), a huge robot from a bygone era.
Fellow robots Sparx (voice of MATT LUCAS), Robotsky (voice of BILL NIGHY) and Mike the Fridge (voice of DAVID BOWERS), who are the sole members of the Robot Revolutionary Front, know what the robot boy really is and want his help to defeat Hamegg. But with President Stone wanting the Blue Core inside him so that he can wage war with those on the planet below him -- to get reelected -- Astro Boy must contend with all of that while also facing the dangerous and continuously morphing Peacekeeper robot.