In a future where robots are integrated into everyday human society, a brilliant but grieving scientist named Dr. Tenma creates a powerful robot boy to replace his deceased son, Tobio. This boy, who will come to be known as Astro, is built with incredible abilities, including rocket boosters in his arms and legs, super strength, and advanced sensory capabilities. However, Dr. Tenma soon becomes disheartened when the robot child cannot grow or truly replicate his lost son, leading him to abandon the creation.

The story varies across the different anime productions, but a central narrative arc finds the abandoned robot boy falling into the hands of a cruel circus owner named Hamegg, who forces him to perform. Eventually, the kind-hearted Professor Ochanomizu, the head of the Ministry of Science, rescues Astro. The professor becomes Astro's legal guardian and mentor, guiding him as he learns to use his powers to protect both humans and robots from various threats, including criminals, robots that have gone berserk, and alien invaders.

The original 1963 black-and-white series, produced by Mushi Productions, is where this story first came to life and it established the core conflict of a robot seeking acceptance and fighting for justice in a world that often fears him. The 1980 series, a color remake, places the story in the year 2030 and adopts a darker tone, focusing more on Astro's robotic nature and featuring a recurring villain named Skunk who steals the blueprints for Astro's design. In this version, after being disowned by Dr. Tenma, Astro is tricked into signing a contract with Hameggs Robot Circus, where he is renamed Astro Boy and eventually meets Professor Ochanomizu.

The 2003 reboot reimagines the story for a new generation, setting it in the year 2043. This series heavily serializes the narrative, following Astro as he adjusts to life with Professor Ochanomizu while being stalked by his original creator, Dr. Tenma. A major narrative arc involves a growing conflict between an anti-robot movement led by a politician named Acetylene Lamp and a robot uprising spearheaded by a figure known as the Blue Knight, who seeks to create an independent robot nation. Throughout this series, Astro is equipped with the Kokoro program, a unique artificial intelligence that grants him genuine human emotions, which becomes central to his struggle to find his own identity and broker peace between humans and machines.