Season 1
- More than Meets the Eye 1-3
- Transport to Oblivion
- Roll for It
- Divide and Conquer
- Fire in the Sky
- S.O.S Dinobots
- Fire on the Mountain
- War of the Dinobots
- The Ultimate Doom 1-3
- Countdown to Extinction
- A Plague of Insecticons
- Heavy Metal War
Season 2
- Autobot Spike
- Changing Gears
- City of Steel
- Attack of the Autobots
- Traitor
- The Immobilizer
- The Autobot Run
- Atlantis, Arise!
- Day of the Machines
- Enter the Nightbird
- A Prime Problem
- The Core
- The Insecticon Syndrome
- Dinobot Island 1-2
- The Master Builders
- Auto Berserk
- Microbots
- Megatron's Master Plan 1-2
- Desertion of the Dinobots 1-2
- Blaster Blues
- A Decepticon Raider in King Arthur's Court
- The Golden Lagoon
- The God Gambit
- Make Tracks
- Child's Play
- Quest for Survival
- The Secret of Omega Supreme
- The Gambler
- Kremzeek!
- Sea Change
- Triple Takeover
- Prime Target
- Auto-Bop
- The Search for Alpha Trion
- The Girl Who Loved Powerglide
- Hoist Goes Hollywood
- The Key to Vector Sigma 1-2
- Aerial Assault
- War Dawn
- Trans-Europe Express
- Cosmic Rust
- Starscream's Brigade
- The Revenge of Bruticus
- Masquerade
- B.O.T.
- For the Japanese post-Season Two continuation, see Transformers: Scramble City
- For the Western post-Season Two continuation, see The Transformers: The Movie
Season 3
- Five Faces Of Darkness 1-5
- The Killing Jar
- Chaos
- Dark Awakening
- Forever Is A Long Time Coming
- Starscream's Ghost
- Thief In The Night
- Surprise Party
- Madman's Paradise
- Nightmare Planet
- Ghost In The Machine
- Webworld
- Carnage In C-Minor
- The Quintesson Journal
- The Ultimate Weapon
- The Big Broadcast Of 2006
- Fight Or Flee
- The Dweller In The Depths
- Only Human
- Grimlock's New Brain
- Money Is Everything
- Call Of The Primitives
- The Face of the Nijika
- The Burden Hardest To Bear
- The Return Of Optimus Prime 1-2
- For the Japanese post-Season Three continuation, see Transformers: ★Headmasters.
