Set in a fictional spacefaring universe, the story follows Shiki Granbell, a boy with gravity powers who embarks on a voyage aboard the titular starship in search of a cosmic entity named Mother.

His adoptive grandfather, the benevolent "Demon King" robot Ziggy, teaches him to control gravity with a superhuman power called Ether Gear.

Ten years after Ziggy's death, the park is visited by spacefaring content creators Rebecca Bluegarden and Happy, whom Shiki befriends when the dying robots force the three off Granbell before expending their vital Ether energy.

Meanwhile, Rebecca develops her own Ether Gear ability to reverse time and travel between parallel universes to save Shiki after he is killed by the crime lord Drakken Joe.

Before leaving the Sakura Cosmos, the Edens Zero crew encounters a revived, malevolent Ziggy, who wishes for machines to rule the universe by ensuring Mother's death in the near future, which would trigger an extinction event for all human life.

Following a three-year conflict, Shiki discovers Ziggy's identity as his own alternate self who tried stopping the bombs, an act resulting in his and Rebecca's Ether Gear creating a spacetime distortion that sent them 20,000 years into the future.

Pino realizes Ziggy is being controlled when he discreetly repairs her memory, allowing her to access an empowered Overdrive state and free him with her EMP.

Upon recalling their future, they find Universe Zero to be an idyllic world where Witch, Valkyrie, Ziggy, and many other deceased figures are alive, and various misfortunes such as the Granbell robots' Ether shortage have never occurred.

[7] Although the title is the name of the main characters' spaceship, Mashima revealed that he thought of a deeper meaning for it, but that its usage would depend on future developments of the story.

[8] When developing the idea for his next series, Mashima originally anticipated using another sword and sorcery setting similar to his previous manga, but decided on creating a "space fantasy" adventure due to a lack of such contemporary shōnen manga; he coined the term "space fantasy" from his own misinterpretation of "SF", the abbreviation of science fiction in Japan, as a child.

[10] In 2021, Mashima stated that Edens Zero would continue the themes of friendship, family, and battles from Fairy Tail, but that it may change slightly by the end when the mystery of the character Mother is revealed.

[7][17] North American publisher Kodansha USA has released chapters of the series on digital platforms such as Crunchyroll Manga and Amazon Kindle.

[19] At the Tokyo Game Show livestream on September 26, 2020, it was revealed that the anime would be produced by J.C.Staff and directed by Yūji Suzuki, with Shinji Ishihira serving as chief director, Mitsutaka Hirota overseeing scripts, Yurika Sako designing the characters, and Yoshihisa Hirano composing the music.

Amy McNulty gave the volume a 3.5 rating, calling it a "solid start" and praising the story's pacing, characters, and art, while adding that it "may not blow anyone away".

Faye Hopper, who gave the volume a 3 rating, found that the shift from "high fantasy pastiche to Star Wars reminiscent sci-fi" helped enrich the story, but criticized Mashima's humor and adherence to shōnen manga conventions.

Teresa Navarro gave it a 2 rating, finding the characters and art style to be nearly identical to those in Fairy Tail, but considering its potential to gain a cult following from fans of the shōnen genre.