In a remote desert on the planet Zi, a boy named Van stumbles upon an abandoned, dilapidated facility. Inside, he discovers an opaque cocoon that cracks on its own, releasing a dinosaur‑like robot known as an Organoid. Van names the creature Zeke and takes it under his care. Soon, a group of bandits arrives, intent on seizing the Organoid. The bandits wield Zoids, beast‑like mechanical units used for combat. With the help of an old Zoid called the Shield Liger, which Van revives and fuses with, he manages to fend off the attackers. Returning to the facility with Zeke, Van finds another cocoon and hopes for yet another Organoid. When it breaks, however, a girl emerges instead. She knows only her name, Fiona, and that she must locate an object called the Zoid Eve. Determined to uncover the mystery of her existence, Fiona joins Van and Zeke on their journey. Together, the trio encounters many allies and adversaries, faces various dangers, and experiences moments of light‑heartedness as they travel.