In the desolate expanse of Planet Zi's desert, a young boy named Van stumbles upon a forsaken structure housing a mysterious cocoon. From this cocoon emerges an enigmatic dinosaur-like robot known as an 'Organoid,' whom Van affectionately dubs Zeke. However, Van's claim over Zeke attracts the attention of a band of marauders piloting formidable mechanical beasts called 'Zoids.' In a bid to protect his newfound companion, Van merges with an ancient Zoid, the 'Shield Liger,' and repels the attackers. Upon revisiting the facility with Zeke, Van encounters yet another cocoon, but this time it hatches a bewildered girl named Fiona. With a sole recollection of her quest to find the elusive 'Zoid Eve,' Fiona joins Van and Zeke in a quest filled with peril and mystery. Together, they traverse this unfamiliar world, encountering allies and adversaries, unraveling the enigma of Fiona's purpose, and pursuing the truth behind the legendary Zoid Eve amid moments of camaraderie and danger.