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.
1. "Commence Battle - Attack Liger Zero"
2. "New Partners vs. Naomi the Red Comet"
3. "The Prince Arrives - Harry Champ"
4. "Illegal Battle - The Mysterious Backdraft Group"
5. "High Speed Battle - Transforming into Zero Jager"
6. "The Dark Giant - The Invincible Elephander"
7. "The Desert Gang - The Hovercargo's in Danger"
8. "Invasion of the Fierce Tigers - Transform to Zero Schneider"
9. "The Princess Arrives - Mary Champ"
10. "Desert Tusk - Assault of the War Sharks"
11. "The Sensational Three - Rematch with Jack Sisco"
12. "Zero is Stolen - The Fiery Battle"
13. "The Brave Wild Eagle - The Raynos vs. The Zabat"
14. "Frightday the 13th"
15. "Laon Returns - Anti-gravity Catastrophy"
16. "The Red Rival - Leon Toros Returns"
17. "Warriors on Vacation - The Storm Sworders"
18. "Love on the Battlefield - My Love, the Judge"
19. "The Third Conversion - Zero Panzer's Debut"
20. "The Shadow Fox - Brad's Betrayal"
21. "Harry's Disaster - Dr. Laon Traps Toros"
22. "The Dragon Under the Sea - In Search of the Ultimate X"
23. "The Dragon Awakens - The Berserk Fury Enters the Fray"
24. "The Tournament of Heroes - The Royal Cup"
25. "Survival - The Mystery of the Ultimate X"
26. "The Miracle of Zero - The Wind, the Cloud, and Adventure"