Zoids Chaotic Century is about a boy named Van. Van is out in the desert somewhere and is being chased by three rowdy bandits trying to shoot him down for no reason. He ends up wandering inside some ruins that he finds and tries to fix his broken hover board so he can get back to the colony. After one of the bandits gets himself trapped Van wanders into a secret room that wasn't there before. Inside the room Van finds two green stasis pods that are in the middle of the room. Van walks up to them and tries to figure out what they are. He accidentally presses a button on one of the pods and they begin to crack. Inside one of the pods is a silver organoid that immediately wacks Van into a wall. Van gets back up and greets his new friend who he calls Zeke. He named him Zeke after his father's Command Wolf which was also called Zeke. In the other pod is a little girl that can't seem to remember much of anything. The first word she says is Fiona and Van suspects that is her name. He decides to call her Fiona because of that. Son after that the bandits break through the wall of that room Zeke takes them both and they go to an old and abandoned Shield Liger they find in the desert and Zeke ressurects it. Then they fight off the bandits that tried to kill Van.

Now Van, Fiona, and Zeke head back to the village and then some bandits try to kidnap Zeke because they believe that he is an organoid. Then Van gets tied up because he tried to go after them. Later after Fiona releases him they go after the bandits. After they take care of the bandits they get Maria, Van's sister, and Zeke back and then start out on a quest to find something Fiona thinks will restore her memory. The Zoid Eve, is some where and they need to go and find it.

Although they don't know it yet they will eventually find themselves in the middle of a war between the Helic Republic and the Guylos Empire. Regent Prozen tries to take the throne from Rudolph and Hilts brings the ultimate Death Saurer back to life. In the end all is well with Planet Zi and everyone is happy again. The ultimate evil will be destroyed and it will be thanks to Thomas, Van, Fiona, Moonbay, Irvine, and the rest of the gang.