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 Zoid Battle Commission seems to be a significant power on Planet Zi, fielding a considerable arsenal of armed Zoids, orbital platforms serviced by their own launch facilities as well as orbital based weapons systems. It is not made clear in the series if the Helic Republic and Guylos Empire still exist, although the final battle upon the rusted Ultrasaurus, hinted to be same one in Zoids: Chaotic Century, could suggest neither were left, and people had free rein to battle in old battlefields.

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.