| # | Title | Writer | Original Broadcast Date (US) |
| 1 | Cybertron City | Akira Okeya | 31/01/2004 |
| 2 | Energon Stars | Akira Okeya | 07/02/2004 |
| 3 | Scorpinok | Shōji Tonoike | 14/07/2004 (Misspelling in the title card) |
| 4 | Megatron's Sword | Shōji Tonoike | 21/02/2004 |
| 5 | The New Cybertron City | Shōji Tonoike | 28/02/2004 |
| 6 | Megatron Resurrected | Akira Okeya | 06/03/2004 |
| 7 | Megatron Raid | Akira Okeya | 13/03/2004 |
| 8 | Starscream the Mysterious Mercenary | Shōji Tonoike | 09/04/2004 |
| 9 | Battle of the Asteroid Belt | Akira Okeya | 09/04/2004 |
| 10 | Energon Tower | Shōji Tonoike | 09/04/2004 |
| 11 | The Legend of Rodimus | Akira Okeya | 09/04/2004 |
| 12 | Crisis in Jungle City | Shōji Tonoike | 18/06/2004 |
| 13 | Kicker Beware! | Akira Okeya | 25/06/2004 |
| 14 | Energon Grid | Akira Okeya | 01/07/2004 |
| 15 | Rodimus: Friend or Foe? | Akira Okeya | 02/07/2004 |
| 16 | Go for Unicron! | Shōji Tonoike | 03/07/2004 |
| 17 | The Return of Demolishor | Akira Okeya | 03/07/2004 |
| 18 | A Tale of Two Heros | Akira Okeya | 03/07/2004 (Misspelling in the title card) |
| 19 | Battle Stations | Shōji Tonoike | 03/07/2004 |
| 20 | Alpha Q: Identity | Akira Okeya | 03/07/2004 |
| 21 | Shockblast: Rampage | Akira Okeya | 03/07/2004 |
| 22 | Survival Instincts | Akira Okeya | 27/08/2004 |
| 23 | Each One Fights... | Shōji Tonoike | 03/09/2004 |
| 24 | Unicron Unleashed | Akira Okeya | 04/09/2004 |
| 25 | Open Fire! | Akira Okeya | 04/09/2004 |
| 26 | Ripped Up Space | Akira Okeya | 04/09/2004 |
| 27 | Team Optimus Prime | Akira Okeya | 04/09/2004 |
| 28 | Protection | Akira Okeya | 08/10/2004 |
| 29 | Improsoned Inferno | Akira Okeya | 15/10/2004 (Misspelling in the title card) |
| 30 | Jungle Planet | Akira Okeya | 22/10/2004 |
| 31 | Bulkhead | Shōji Tonoike | 29/10/2004 |
| 32 | Farewell Inferno | Akira Okeya | 05/11/2004 |
| 33 | Scorponok's Scars | Shōji Tonoike | N/A Never aired or dubbed into English |
| 34 | Crash Course | Akira Okeya | 08/11/2004 |
| 35 | Omega Supreme | Shōji Tonoike | 09/11/2004 |
| 36 | A Heroic Battle | Akira Okeya | 10/11/2004 |
| 37 | The Power | Akira Okeya | 11/11/2004 |
| 38 | Optimus Supreme | Shōji Tonoike | 16/11/2004 |
| 39 | Unicron Perishes | Shōji Tonoike | 17/11/2004 |
| 40 | Ambition | Akira Okeya | 31/12/2004 |
| 41 | Wishes | Akira Okeya | 07/01/2005 |
| 42 | Galvatron! | Akira Okeya | 14/01/2005 |
| 43 | Break Through | Shōji Tonoike | 21/01/2005 |
| 44 | Distribution | Akira Okeya | 28/01/2005 |
| 45 | The Omega Train | Akira Okeya | 04/02/2005 |
| 46 | Deception Army | Akira Okeya | 11/02/2005 |
| 47 | Ironhide Team | Akira Okeya | 18/02/2005 |
| 48 | Formidable | Shōji Tonoike | 25/02/2005 |
| 49 | Galvatron Terror | Akira Okeya | 04/03/2005 |
| 50 | Destructive Power | Akira Okeya | 11/03/2005 |
| 51 | Spark | Akira Okeya | 19/03/2005 |
| 52 | The Sun | Akira Okeya | 19/03/2005 |
