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.
| Title | Air Date | Duration | ||
|---|---|---|---|---|
| Season 1 | Episode 1 | The Boy from Planet Zi | 1999-09-04 | 25 min |
| Season 1 | Episode 2 | The Mysterious Fiona | 1999-09-11 | 25 min |
| Season 1 | Episode 3 | Memory | 1999-09-18 | 25 min |
| Season 1 | Episode 4 | The Protectors | 1999-09-25 | 25 min |
| Season 1 | Episode 5 | Sleeper Trap | 1999-10-02 | 25 min |
| Season 1 | Episode 6 | Jump Zeke! | 1999-10-09 | 25 min |
| Season 1 | Episode 7 | The Battle of Red River | 1999-10-16 | 25 min |
| Season 1 | Episode 8 | The Road to the Republic | 1999-10-23 | 25 min |
| Season 1 | Episode 9 | The Valley of the Monster | 1999-10-30 | 25 min |
| Season 1 | Episode 10 | The Mountain of Dreams | 1999-11-06 | 25 min |
| Season 1 | Episode 11 | The Fog at Mt. Iselina | 1999-11-13 | 25 min |
| Season 1 | Episode 12 | The Black Organoid | 1999-11-20 | 25 min |
| Season 1 | Episode 13 | The Battle of Chronos | 1999-11-27 | 25 min |
| Season 1 | Episode 14 | Wake Up! Zeke | 1999-12-04 | 25 min |
| Season 1 | Episode 15 | Deploy the ZG! | 1999-12-11 | 25 min |
| Season 1 | Episode 16 | New Helic City | 1999-12-18 | 25 min |
| Season 1 | Episode 17 | The Longest Night of the Republic | 1999-12-25 | 25 min |
| Season 1 | Episode 18 | The Defense of the City | 2000-01-08 | 25 min |
| Season 1 | Episode 19 | Prozan's Conspiracy | 2000-01-15 | 25 min |
| Season 1 | Episode 20 | The Resurrection Monster | 2000-01-22 | 25 min |
| Season 1 | Episode 21 | The Charged Particle Gun | 2000-01-29 | 25 min |
| Season 1 | Episode 22 | Farewell to a Friend | 2000-02-05 | 25 min |
| Season 1 | Episode 23 | The Imperial Ring | 2000-02-12 | 25 min |
| Season 1 | Episode 24 | A Voice from Afar | 2000-02-19 | 25 min |
| Season 1 | Episode 25 | The New Liger | 2000-02-26 | 25 min |
| Season 1 | Episode 26 | Memories of Zi | 2000-03-04 | 25 min |
| Season 1 | Episode 27 | The Saviour | 2000-03-11 | 25 min |
| Season 1 | Episode 28 | Run, Wolf! | 2000-03-18 | 25 min |
| Season 1 | Episode 29 | Heroes of the Sky | 2000-03-25 | 25 min |
| Season 1 | Episode 30 | Moonbay's Waltz | 2000-04-01 | 25 min |
| Season 1 | Episode 31 | The Three Guards | 2000-04-08 | 25 min |
| Season 1 | Episode 32 | The Doom Machine | 2000-04-15 | 25 min |
| Season 1 | Episode 33 | The Battle for Survival | 2000-04-22 | 25 min |
| Season 1 | Episode 34 | The Capital Ablaze | 2000-04-29 | 25 min |
| Season 2 | Episode 1 | The Secret Mission | 2000-05-06 | 25 min |
| Season 2 | Episode 2 | The Sniper | 2000-05-13 | 25 min |
| Season 2 | Episode 3 | The Blue Devil | 2000-05-20 | 25 min |
| Season 2 | Episode 4 | The Steel Bison | 2000-05-27 | 25 min |
| Season 2 | Episode 5 | The Invisible enemy | 2000-06-03 | 25 min |
| Season 2 | Episode 6 | The Zoid Hunters | 2000-06-10 | 25 min |
| Season 2 | Episode 7 | The Devil's Maze | 2000-06-17 | 25 min |
| Season 2 | Episode 8 | Raven | 2000-06-24 | 25 min |
| Season 2 | Episode 9 | The Emperor's Holiday | 2000-07-01 | 25 min |
| Season 2 | Episode 10 | Assault of the Mega-Monster | 2000-07-08 | 25 min |
| Season 2 | Episode 11 | The Wings of Darkness | 2000-07-15 | 25 min |
| Season 2 | Episode 12 | Devil of the Sea | 2000-10-14 | 25 min |
| Season 2 | Episode 13 | A Monster Awakens | 2000-07-29 | 25 min |
| Season 2 | Episode 14 | The Black Lightning | 2000-08-05 | 25 min |
| Season 2 | Episode 15 | The Distant Stars | 2000-08-12 | 25 min |
| Season 2 | Episode 16 | Attack of the Geno Breaker | 2000-08-19 | 25 min |
| Season 2 | Episode 17 | The Boy from the Ruins | 2000-08-26 | 25 min |
| Season 2 | Episode 18 | Van's New Power | 2000-09-02 | 25 min |
| Season 2 | Episode 19 | Phantom | 2000-09-09 | 25 min |
| Season 2 | Episode 20 | G-File | 2000-09-16 | 25 min |
| Season 2 | Episode 21 | Supersonic Battle | 2000-09-23 | 25 min |
| Season 2 | Episode 22 | Cerberus | 2000-10-07 | 25 min |
| Season 2 | Episode 23 | The Nightmare | 2000-10-14 | 25 min |
| Season 2 | Episode 24 | Attack of the Winged Dragons | 2000-10-21 | 25 min |
| Season 2 | Episode 25 | The Capital Collapses | 2000-10-28 | 25 min |
| Season 2 | Episode 26 | The Giant Fortress | 2000-11-04 | 25 min |
| Season 2 | Episode 27 | The Great Sea Battle | 2000-11-11 | 25 min |
| Season 2 | Episode 28 | The Gravity Cannon | 2000-11-18 | 25 min |
| Season 2 | Episode 29 | The Final Battle | 2000-11-25 | 25 min |
| Season 2 | Episode 30 | The Ancient Memory | 2000-12-02 | 25 min |
| Season 2 | Episode 31 | The Zoid Eve | 2000-12-09 | 25 min |
| Season 2 | Episode 32 | The Moment of Annihilation | 2000-12-16 | 25 min |
| Season 2 | Episode 33 | Return to Another Tomorrow | 2000-12-23 | 25 min |
