Atom is attending a party on the space station with Dr. Ochanomizu. However, while at the party, he hears a voice. It is the voice of a robot that had been abandoned by someone. The abandoned robot is a security guard robot named Ivan, and after being refueled with energy, Ivan sets off on a journey to find his owner, Minya.

Astro Boy, helping Professor Ochanomizu with planetary exploration, discovers a trash star floating in space. On this star, robots that can no longer move have been thrown away stacked on top of each other. On this robot mountain, Astro saves a robot soldier, Bemu, that escaped from the verge of death and takes him back to Earth. "I'm tried of fighting!" "I feel the same." While Atom and Bemu are together, a warm friendship is born and goes on to deepen. However, one day, the trash star draws near to the Earth. If it hits, the Earth would have a huge explosion. The Earth is in chaos. As this happens, there is just one way to stop the crash into Earth. Only this is... What will Astro do. Will he be able to protect a peaceful Earth as well as his friendship with Bemu?

The film begins with the Phoenix retelling the tales and hopes of Astro Boy. Many of the visual being directly taken from the 1980s TV series as it recaps some of his adventures. Following this recap, Astro Boy confronts Blue Bon and tries to convince him to change his mind about the humans. But Blue Bon misunderstands, assuming that if Astro Boy does not agree then he is an enemy. Blue Bon hates humans because they broke apart his family (Maria and Tonto). A battle begins between the two after Astro Boy fails to convince Blue Bon that they aren't each others' enemy.

Compilation of Episodes 46, 56 and 71 from the 1963 Astro Boy series that were reproduced in color for this theater version.

The Phoenix asks us why humans choose war as a means of solving problems, while it looks back on the history of Kyoto and ponders on the riot at Ikeda-ya by the Shinsen-gumi in the last days of the Tokugawa regime.

Doctor Tenma, chief of the Ministry of Science, brought a digital brain genome from an aircraft. Doctor Tenma begins a trip to Mars, then combines the genome with a robot. Doctor Tenma's son, Tobio, who had died in a traffic accident, has been revived.

The interplanetary spacecraft Galileo II carries Atom and his friends to Titan, a satellite of Saturn. However, what awaits them when they arrive there is an attack from an unknown entity. What appears is a mechanical life form called "Igza" that wants to destroy humans. The battle between Atom and Igza unfolds in the far reaches of space.

A boy is chased by a robot through some ruins. There, he finds an Earth ruled by a computer called "Gaia," who has lost patience with humans who repeatedly cause war and environmental destruction. While desperately trying to escape, the boy discovers Atom, which had been put on display 200 years ago after it had finished its role.