| # | Title | Original airdate | Prod. code |
| 1 | "The Reformatting" | | |
| The Maximals awaken on their homeworld of Cybertron, with no memory of how they got there. Unable to Transform, they are hunted down by mindless vehicle Transformer drones. |
| 2 | "Master of the House" | | |
| The Maximals learn how to transform and gain access to the Council Citadel. There, they learn that Megatron has taken over the planet and intends to wipe out all organic life. |
| 3 | "Fires of the Past" | | |
| While searching for clues to their missing memories, Black Arachnia and Rattrap encounter Jetstorm, Thrust and Tankor - three deadly new Vehicon Generals created by Megatron. |
| 4 | "Mercenary Pursuits" | | |
| As the Vehicon Generals continue to hunt the Maximals, Rattrap discovers a counter-virus that helps him Transform - but once he starts, he can't stop. |
| 5 | "Forbidden Fruit" | | |
| The Maximals discover a new Beast Mode Maximal - a bat named Nightscream - and a mysterious fruit tree, neither of which should exist on the machine world of Cybertron. |
| 6 | "The Weak Component" | | |
| Rattrap finally learns how to Transform, only to discover his Robot Mode has no weapons. With nowhere else to turn for protection, he strikes a deal with Megatron. |
| 7 | "Revelations, Part 1: Discovery" | | |
| The Maximals discover a junkyard facility where the robot shells of the missing Transformers are stored. Meanwhile, Black Arachnia and Thrust discover a fatal attraction for one another. |
| 8 | "Revelations, Part 2: Descent" | | |
| Cheetor leads a dangerous mission to try and bring out Tankor's old Maximal personality. In doing so, Rattrap discovers a major clue to the Maximal's missing memories. |
| 9 | "Revelations, Part 3: Apocalypse" | | |
| Nightscream fights to retrieve Black Arachnia's stolen Spark. Meanwhile, Optimus is able to contact Rhinox's Spark, but Rhinox deals him a major surprise. |
| 10 | "Survivor" | | |
| Megatron sends his Generals and Diagnostic Drone into the catacombs to kidnap Nightscream and learn the secret behind his Beast Mode. Nightscream is forced to relive a painful memory from his past. |
| 11 | "Techno-Organic War, Part 1: The Key" | | |
| Tankor uncovers an ancient weapon with the power to turn organic material into cybernetic metal. Nightscream gets hit by the weapon and the Maximals race against time to save him from going off-line. |
| 12 | "Techno-Organic War, Part 2: The Catalyst" | | |
| Rattrap uncovers a catalyst program that speeds up the growth of Cybertron's newfound plant life. Meanwhile, Black Arachnia discovers the truth about Thrust's Spark. |
| 13 | "Techno-Organic War, Part 3: End of the Line" | | |
| Megatron prepares a doomsday weapon that can wipe out everything organic on Cybertron - including the Maximals. Meanwhile, Optimus discovers his own doomsday weapon... |
| # | Title | Original airdate | Prod. code |
| 14 | "Fallout" | | |
| Having destroyed his world, Optimus must face the consequences before The Matrix. Written by: Robert N. Skir & Marty Isenberg, Directed by: Raul Sanchez Inglis |
| 15 | "Savage Noble" | | |
| While trying to recruit the Vehicons, the Maximals discover themselves being stalked by an all-new threat. Written by: Len Wein, Directed by: Greg Donis |
| 16 | "Prometheus Unbound" | | |
| The Maximals attempt to infiltrate Megatron's former fortress, only to have their mission threatened by their supposed new ally! Written by: Marv Wolfman, Directed by: Sebastion Brown |
| 17 | "In Darkest Knight" | | |
| Black Arachnia finally revives Silverbolt... but is he glad to be reawakened? Written by: Steven Melching, Directed by: George Samilski |
| 18 | "A Wolf In The Fold" | | |
| While also defending themselves against Megatron, the Maximals face their most recent dangerous enemies - each other! Written by: Brynne Chandler Reaves, Directed by: William Lau |
| 19 | "Home Soil" | | |
| A seemingly empty spaceship crashes onto Cybertron, unleashing a dangerous entity! Written by: Meg McLaughlin, Directed by: Dennis Heaton |
| 20 | "Sparkwar Part One: The Strike" | | |
| The Maximals defeat Thrust and his cycle drones...again, and Megatron Makes 2 new Generals Written by: Brooks Wachtel, Directed by: Steve Sacks |
| 21 | "Sparkwar Part II: The Search" | | |
| Optimus has a vision - a short glimpse at the locations of the captured sparks. Written by: Michael Reaves, Directed by: Gino Nichele |
| 22 | "Sparkwar Part III: The Siege" | | |
| Optimus and the others move in to free the sparks, as Megatron begins to devour them... Written by: Steven Melching, Directed by: Luke Carroll |
| 23 | "Spark of Darkness" | | |
| Megatron is gone, but things are far from peaceful as old robot attacks the Maximals. Written by: Nick Dubois, Directed by: Greg Donis |
| 24 | "Endgame Part I: The Downward Spiral" | | |
| Megatrons fortress crashes down after losing power. Rattrap's unauthorized action saves Botanica, but hastens the crash. Written by: Michael Reaves, Directed by: Angela Stevenson |
| 25 | "Endgame Part II: When Legends Fall" | | |
| Written by: Steven Melching, Directed by: George Samilski |
| 26 | "Endgame Part III: Seeds of The Future" | | |
| The drones prepare the sparks for Megatron to absorb and Primal remains the only other Transformer |
