In the desolate landscape of Planet Zi, a young boy named Van stumbles upon a dilapidated establishment where he uncovers an enigmatic cocoon that eventually hatches into Zeke, an Organoid that resembles a dinosaur. Despite Van's claim of ownership, a band of marauders, armed with Zoids - mechanical monsters constructed for combat - chases him relentlessly with the intention of pilfering Zeke. In a bid to safeguard himself, Van melds with an ancient Shield Liger Zoid and confronts the bandits. Upon his return with Zeke, Van locates another cocoon on the premises, hoping to acquire another Organoid. Instead, he finds Fiona, a girl with a hazy memory and a mission to expose the "Zoid Eve." Along with Van and Zeke, Fiona sets course for a voyage full of hazard, excitement, and self-discovery. They face both allies and adversaries, accumulating experiences of both risk and pleasure along the way.