Shiki Granbell is a human Ether Gear user who lives among robots on the planet Granbell, a deserted theme park world in the Sakura Cosmos. One day, the park is visited by two space traveling B-Cubers – Rebecca Bluegarden and her robotic cat companion Happy – whom Shiki befriends while they are recording videos for their online account, Aoneko Channel. After the park's robots force them off the planet to save Shiki from being stranded before their batteries die, the three set out to explore the universe by searching for Mother, the fabled goddess of the cosmos, who is said to grant any wish. Early in Shiki's journey, the space pirate Elsie Crimson gifts him with the interstellar warship Edens Zero as inheritance from the mechanical Demon King Ziggy, Shiki's deceased grandfather figure. In preparation for the voyage, Shiki searches the Sakura Cosmos for the Demon King's Four Shining Stars, Ziggy's android crewmates whose functions are connected to those of Edens Zero. He also recruits other friends he encounters in the process: Weisz Steiner, a criminal from another reality created by the Chronophage; E.M. Pino, a young android built by Ziggy who suffers from memory damage; and Homura Kōgetsu, a swordswoman and successor to one of the Shining Stars. After assembling the Four Shining Stars and defeating the crime lord Drakken Joe, the crew returns to Granbell to discover a reactivated Ziggy, who has become malevolent and desires to conquer humans for their mistreatment of robots. Avoiding destruction from Ziggy's enhanced Edens One warship, the Edens Zero crew race against Ziggy to prevent him from reaching Mother, and to protect humans and robots that are affected by his genocidal actions.