On the remote desert world of Planet Zi, a boy named Van stumbles upon a ruined, abandoned facility. Within, he discovers an opaque cocoon that ruptures on its own, releasing a dinosaur-like robot known as an "Organoid." Van names the creature Zeke and takes possession of it, but a gang of bandits pursues him to steal the Organoid. These bandits wield "Zoids," beast-like mechanical units designed for combat. Van manages to repel his attackers by awakening and merging with an old Zoid called the "Shield Liger." Van goes back to the facility with Zeke and uncovers another cocoon. He is thrilled at the prospect of acquiring a second Organoid, but when the shell breaks, a girl emerges instead. Knowing nothing of her past, the girl recalls only that her name is Fiona and that she must find an object known as the "Zoid Eve." Driven to unravel the mystery of her existence, Fiona sets out with Van and Zeke to discover the true nature of the Zoid Eve. During their journey, the trio meets numerous allies and enemies, facing various perils while also sharing moments of levity.