| # | Title | Western Title | Writer | Broadcast Date (Japan) |
| 1 | We're Back! | Aftermath | Larry DiTillio | 06/10/1999 |
| 2 | Enter the New Warriors! Snippety-snip, Sir! | Coming of the Fuzors, Part 1 | Bob Forward | 13/10/1999 |
| 3 | Convoy Reborn | Coming of the Fuzors, Part 2 | Bob Forward | 20/10/1999 |
| 4 | Grand-Slam Tarans | Tangled Web | Len Wein | 27/10/1999 |
| 5 | I Quit! | Maximal, No More | Patrick Barry | 03/11/1999 |
| 6 | Huh? The Flower? | Other Visits, Part 1 | Larry DiTillio | 10/11/1999 |
| 7 | Huh? The Face? | Other Visits, Part 2 | Larry DiTillio | 17/11/1999 |
| 8 | Farewell! | Code of Hero | Ian Weir | 24/11/1999 |
| 9 | I'm a Crab! | Transmutate | Christy Marx | 01/12/1999 |
| 10 | Meyow're Under Arrest | The Agenda, Part 1 | Bob Forward | 08/12/1999 |
| 11 | I Do Love You! | The Agenda, Part 2 | Bob Forward | 15/12/1999 |
| 12 | Once Upon a Time | The Agenda, Part 3 | Bob Forward | 22/12/1999 |
| 13 | Grow Bigger | Optimal Situation | Bob Forward | 29/12/1999 |
| 14 | Remix: Where is the Banana? | Japan Only: Clip Show | - | 05/01/2000 |
| 15 | Rrray! | Deep Metal | Larry DiTillio | 12/01/2000 |
| 16 | Loose-Fitting! | Changing of the Guard | Evan Somers | 19/01/2000 |
| 17 | I Am Resurrected! | Feral Scream, Part 1 | Greg Johnson | 26/01/2000 |
| 18 | Cheetus Arises! | Feral Scream, Part 2 | Jules Dennis | 02/02/2000 |
| 19 | Love Typhoon | Proving Grounds | Arthur Sellers | 09/02/2000 |
| 20 | Zzzap! Tingly Tongly Too! | Go With the Flow | Bob Forward | 16/02/2000 |
| 21 | Sssshiny! | Crossing the Rubicon | D.C. Fontana | 23/02/2000 |
| 22 | Blaze, Dragon | Master Blaster | Eric Torin | 01/03/2000 |
| 23 | I Hath Returned | Other Victories | Larry DiTillio | 08/03/2000 |
| 24 | Ka-Boom | Nemesis, Part 1 | Bob Forward | 15/03/2000 |
| 25 | Happy? This Should Do It | Nemesis, Part 2 | Simon Furman | 22/03/2000 |
| 26 | Remix: I Lost the Banana | Japan Only: Clip Show | - | 29/03/2000 |
| Special (This episode aired Theatrically) | ||||
| - | Beast Wars Metals: Convoy's Great Transformation | Cutting Edge | Ian Weir | 31/7/1999 |
