On the desert planet Zi, a young boy named Van stumbles upon a mysterious facility and awakens Zeke, a unique lifeform called an Organoid.
He soon encounters bandits seeking to steal Zeke, forcing Van to pilot an ancient Zoid, the Shield Liger, for protection.
Back at the facility, Van discovers Fiona, a girl with amnesia who emerges from another cocoon.
Fiona's only clue to her past is the phrase "Zoid Eve," which sets her, Van, and Zeke on a journey to uncover its meaning.
Their adventure takes them across the planet, where they face dangers and forge friendships as they explore the mysteries of Zi and Fiona's true identity.