The show takes place ten years after the finale of Armada, opening in an age of peace on Cybertron and Earth which is destined not to last long. Energon pits the Autobots against an array of villains: the reborn Megatron , the barely functional Unicron, and the mysterious Alpha Q and his Terrorcon minions.
| Title | Time | |
|---|---|---|
| 1 | Cybertron City | 2004-01-09 |
| 2 | Energron Stars | 2004-01-16 |
| 3 | Scorponok | 2004-01-23 |
| 4 | Megatron's Sword | 2004-01-30 |
| 5 | The New Cybertron City | 2004-02-06 |
| 6 | Megatron Resurrected | 2004-02-13 |
| 7 | Megatron Raid | 2004-02-20 |
| 8 | Starscream the Mysterious Mercenary | 2004-02-27 |
| 9 | Battle of The Asteroid Belt | 2004-03-05 |
| 10 | Energon Tower | 2004-03-12 |
| 11 | The Legend of Rodimus | 2004-03-19 |
| 12 | Crisis In Jungle City | 2004-03-26 |
| 13 | Kicker Beware | 2004-04-02 |
| 14 | Energon Grid | 2004-04-09 |
| 15 | Rodimus: Friend or Foe | 2004-04-16 |
| 16 | Go For Unicron | 2004-04-23 |
| 17 | The Return of Demolisher | 2004-05-07 |
| 18 | A Tale of Two Heroes | 2004-04-30 |
| 19 | Battle Stations | 2004-05-07 |
| 20 | Alpha Q: Identity | 2004-05-14 |
| 21 | Shockblast: Rampage | 2004-05-28 |
| 22 | Survival Instincts | 2004-06-04 |
| 23 | Each One Fights... | 2004-06-11 |
| 24 | Unicron Unleashed | 2004-06-18 |
| 25 | Open Fire! | 2004-06-25 |
| 26 | Ripped Up Space | 2004-07-09 |
| 27 | Team Optimus Prime | 2004-07-09 |
| 28 | Protection | 2004-07-16 |
| 29 | Imprisoned Inferno | 2004-07-23 |
| 30 | Jungle Planet | 2004-07-30 |
| 31 | Bulkhead | 2004-08-06 |
| 32 | Farewell Inferno | 2004-08-13 |
| 33 | Scorponok's Scars | 2004-08-20 |
| 34 | Crash Course | 2004-08-27 |
| 35 | Omega Supreme | 2004-09-03 |
| 36 | A Heroic Battle | 2004-09-10 |
| 37 | The Power | 2004-09-17 |
| 38 | Optimus Supreme | 2004-09-24 |
| 39 | Unicron Perishes | 2004-10-01 |
| 40 | Ambition | 2004-10-08 |
| 41 | Wishes | 2004-10-15 |
| 42 | Galvatron! | 2004-10-22 |
| 43 | Break Through | 2004-10-29 |
| 44 | The Omega Train | 2004-11-05 |
| 45 | Deception Army | 2004-11-12 |
| 46 | Ironhide Team | 2004-11-19 |
| 47 | Formidable | 2004-11-26 |
| 48 | Galvatron Terror | 2004-12-03 |
| 49 | Destructive Power | 2004-12-10 |
| 50 | Spark | 2004-12-17 |
| 51 | The Sun | 2004-12-24 |
