Van discovers a Zoid Organoid in an abandoned laboratory while running from two strangers piloting Zoids. Also in the laboratory, in an animated suspension tube is a strange girl. He breaks the tube open and takes her and the Organoid with him. The girl, who says her name is Fiona, wants to find something called "Zoids Eve", and so Van, the Organoid Zeke, and Fiona begin their adventure.
In the 21st century planet Earth was rendered inhospitable to life, and people mass-migrated to Planet Zi, the natural home of metallic life forms known as Zoids. Many years later, Zi faces its end. Its inhabitants partake the journey to migrate back to Earth. Attempting to regenerate the Earth to make it hospitable, the migrants come up with a "Zi-Forming" scheme. However, the plan fails and Earth is left in its state of turmoil. Overrun by Zoids and blanked by unstable weather phenomena, the migrants are faced with a difficult life. The Empire and Republic settlements attempt to uncover Zoids buried within the Earth to bolster their respective armies. The story picks up following second-generation Earth citizens: Leo Conrad and Buzz Cunningham, who have a chance encounter with a girl Sally Land as she flees the clutches of the Empire.
A quest for freedom and legendary treasure begins when a cheerful young adventurer follows his father's footsteps to become the greatest Zoids hunter.
R.D. is a delivery boy who works for a company called Mach Storm in order to earn money to search for the legendary Alpha Zoid. A Zoid that he heard rumours about from his dad that he passionately believes in. Mach Storm also doubles as a Zoid Battling team. In R.D.'s first Coliseum Zoid Battle, he encounters a team that can fuse Zoids. R.D. soon discovers that he has a Zoid that can computably fuse with his Zoid, Liger Zero. After this happens R.D.'s adventure to discover the truth about the Alpha Zoid begins.
Young Ruuji Familon finds a Liger-type Zoid during a salvage mission. Initially, the village is attacked by Bio-Raptor Bio-Zoids, and later a Bio-Megaraptor. After the village generator is destroyed in combat, Ruuji takes the Murasame Liger Zoid and leaves the village alongside Ra-Kan and Rei Mii to find a generator mechanic or the village will be destroyed. Through his journey Ruuji learns he must fight against Digald.
New Century Zero takes place a long time after the events of Zoids: Chaotic Century. Zoids are no longer used for warfare; instead, the combative natures of both Zoids and humans are focused and contained by a series of battle-competitions and tournaments, run by the Zoid Battle Commission.
The series focuses on the Blitz Team, in particular the actions of the Liger Zero and Bit Cloud. The series charts the rise of the Blitz Team through various competitions of the Zoid Battle Commission, and the team's efforts to avoid conflict with the criminal organization known as the Backdraft Group.