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.