Planet Zi, a world where warrior bio-machine lifeforms called Zoids live. They are controled by human pilots in a war with the Republic and the Guylos Empire. One day a boy named Van being cased by bandits hides in some old ruins, he finds two pods in a hidden room & opens one to find out its an odd dragon-like Zoid called an Organoid which he names Zeke.

Zeke then ressurects an old dead blue Shield Liger Zoid for Van to pilot. When Van opens the 2nd pod a very mysterious girl named Fiona comes out of it. They go on the adventure to find more about her past & to find the Zoid Eve, they meet new friends & they get into some serious problems including the war which they try to stop.