| # | Title | Western Title | Writer | Broadcast Date (Japan) |
| 1 | Surface! Ocean City | Cybertron City | Akira Okeya | 09/01/2004 |
| 2 | Shine! Energon Star | Energon Stars | Akira Okeya | 16/01/2004 |
| 3 | Mega Zarak's Trap | Scorpinok | Shōji Tonoike | 23/01/2004 |
| 4 | Proof of Megatron | Megatron's Sword | Shōji Tonoike | 30/01/2004 |
| 5 | A New Cybertron City | The New Cybertron City | Shōji Tonoike | 06/02/2004 |
| 6 | Resurrection! Galvatron | Megatron Resurrected | Akira Okeya | 13/02/2004 |
| 7 | Destron Invasion! | Megatron Raid | Akira Okeya | 20/02/2004 |
| 8 | The Mysterious Assassin Nightscream | Starscream the Mysterious Mercenary | Shōji Tonoike | 27/04/2004 |
| 9 | The Asteroid Belt's Battle to the Death | Battle of the Asteroid Belt | Akira Okeya | 05/03/2004 |
| 10 | Appear! Energon Tower | Energon Tower | Shōji Tonoike | 12/03/2004 |
| 11 | This Tiny Universe | The Legend of Rodimus | Akira Okeya | 19/03/2004 |
| 12 | Crisis of Jungle City | Crisis in Jungle City | Shōji Tonoike | 26/03/2004 |
| 13 | Kicker Targeted | Kicker Beware! | Akira Okeya | 02/04/2004 |
| 14 | Energon Grid Engaged | Energon Grid | Akira Okeya | 09/04/2004 |
| 15 | Enemy? Ally? Rodimus Convoy | Rodimus: Friend or Foe? | Akira Okeya | 16/04/2004 |
| 16 | Target! Unicron | Go for Unicron! | Shōji Tonoike | 23/04/2004 |
| 17 | A Rain of Dinobots! | The Return of Demolishor | Akira Okeya | 30/04/2004 |
| 18 | Confrontation! Two Convoys | A Tale of Two Heros | Akira Okeya | 07/05/2004 |
| 19 | Terror! Unicron Activates | Battle Stations | Shōji Tonoike | 14/05/2004 |
| 20 | Alpha Q's True Identity | Alpha Q: Identity | Akira Okeya | 21/05/2004 |
| 21 | Rampage! Laserwave | Shockblast: Rampage | Akira Okeya | 28/05/2004 |
| 22 | Out of Control! The Starving Unicron | Survival Instincts | Akira Okeya | 04/06/2004 |
| 23 | Respective Battles | Each One Fights... | Shōji Tonoike | 11/06/2004 |
| 24 | Ah! Now It Is Possible | Unicron Unleashed | Akira Okeya | 18/06/2004 |
| 25 | Gale! Wing Saber | Open Fire! | Akira Okeya | 25/06/2004 |
| 26 | Ripped Up Space | Ripped Up Space | Akira Okeya | 02/07/2004 |
| 27 | Team Convoy's Whereabouts | Team Optimus Prime | Akira Okeya | 09/07/2004 |
| 28 | The Planets that Must Be Protected | Protection | Akira Okeya | 16/07/2004 |
| 29 | Imprisoned Inferno | Improsoned Inferno | Akira Okeya | 23/07/2004 |
| 30 | Hellfire! Jungle Planet | Jungle Planet | Akira Okeya | 30/07/2004 |
| 31 | Crucial Moment! Sprung Steps Forward | Bulkhead | Shōji Tonoike | 06/08/2004 |
| 32 | Saraba Inferno | Farewell Inferno | Akira Okeya | 13/08/2004 |
| 33 | Return! Our Scorponok | Scorponok's Scars | Shōji Tonoike | 20/08/2004 |
| 34 | Special Training! Roadbuster | Crash Course | Akira Okeya | 27/08/2004 |
| 35 | Ancient Sage - Omega Supreme | Omega Supreme | Shōji Tonoike | 03/09/2004 |
| 36 | Heroic! Alpha Q's Battle | A Heroic Battle | Akira Okeya | 10/09/2004 |
| 37 | Laserwave's Last Moments | The Power | Akira Okeya | 17/09/2004 |
| 38 | Struggle to the Death! Omega Convoy | Optimus Supreme | Shōji Tonoike | 24/09/2004 |
| 39 | Unicron Extinguished | Unicron Perishes | Shōji Tonoike | 01/10/2004 |
| 40 | Galvatron's Ambition to be Revived | Ambition | Akira Okeya | 08/10/2004 |
| 41 | Superion's Hope | Wishes | Akira Okeya | 15/10/2004 |
| 42 | It's Sinking! Miranda II | Galvatron! | Akira Okeya | 22/10/2004 |
| 43 | Keep Going! Omnicons | Break Through | Shōji Tonoike | 29/10/2004 |
| 44 | A Must See! The Greatest Dream Match: Extra Episode with a Different Airtime | Distribution | Akira Okeya | 03/11/2004 |
| 45 | Roaring Train! Omega Supreme | The Omega Train | Akira Okeya | 05/11/2004 |
| 46 | Scattered, the Destron Army | Deception Army | Akira Okeya | 12/11/2004 |
| 47 | Awesome! Team Roadbuster | Ironhide Team | Akira Okeya | 19/11/2004 |
| 48 | Omega Convoy Once Again | Formidable | Shōji Tonoike | 26/11/2004 |
| 49 | Terrifying! Giant Galvatron | Galvatron Terror | Akira Okeya | 03/12/2004 |
| 50 | Terrifyingly Unprecedented! Super Emperor of Destruction | Destructive Power | Akira Okeya | 10/12/2004 |
| 51 | Power of the Combination Spark | Spark | Akira Okeya | 17/12/2004 |
| 52 | Energon, It Is the Sun | The Sun | Akira Okeya | 24/12/2004 |
