The following list shows the order in which the episodes went into production. This list is interesting as it explains the concentration of 1984 Joes in certain episodes. There is definitely an older tone to the 1984 era episodes, both in terms of the types of stories and the film stock being a little discolored. Several 1985 characters don’t start appearing until Synthoid Conspiracy or later (like Quick Kick, for example). It is also interesting to note that three episodes from Season 2 were slotted into the tail end of the Seaon 1 production order. These episodes (Last Hour to Doomsday, at least) do not feature Serpentor.

The biggest difference from the air date order is found in Season 1, an enormous production block by any account. The five part story to kick off the season, Pyramid of Darkness did not go into production until two thirds of the season had already been completed.

Another note is that the production of the first episodes from the several of the two part stories in Season 1 were not immediately followed by the concluding episode. Obviously, the production order was never intended to be the definitive order in which the animated series was meant to be aired.

Although Duke, Scarlett, Flint and Lady Jaye feature throughout the first season on a recurring basis, it is interesting to note the Joe characters that are featured in early episodes are predominantly from the 1984 Hasbro toyline. This seems to confirm the validity of this production order.

Mini-series 1 – The M.A.S.S. Device ****
4005 The Cobra Strikes
4006 Slaves of the Cobra Master
4007 The Worms of Death
4008 Duel in the Devil’s Cauldron
4009 A Stake in the Serpent’s Heart

Mini-series 2 – The Revenge of Cobra *****
4018 In the Cobra’s Pit
4019 The Vines of Evil
4020 The Palace of Doom
4021 Battle on the Roof of the World
4022 Amusement Park of Terror

Season 1
600-01 Cobra’s Creatures ** (Mutt & Junkyard)
600-02 Countdown for Zartan *** (Spirit, Gung Ho, Doc)
600-04 Cobra Soundwaves (Ace, Airborne)
600-05 Cobra Stops the World ***** (Ace, Torpedo, Deep-Six)
600-06 Jungle Trap ** (Recondo, Rock n’ Roll)
600-07 Haul Down the Heavens *** (Snow Job)
600-08 Battle for the Train of Gold ** (Gung Ho, Wild Bill, Thunder, Short-Fuse)
600-09 Operation Mind Menace ** (Airborne, Flash, Stalker)
600-10 Lights! Camera! Cobra! *** (Shipwreck, Cover-Girl, Recondo)
600-11 Cobra’s Candidate ** (Zap, Spirit)
600-12 Red Rocket’s Glare ** (Roadblock, Recondo)
600-13 Satellite Down * (Spirit)
600-14 Money to Burn *** (Roadblock, Ripcord, Thunder)
600-15 The Phantom Brigade *** (Snow Job, Roadblock, Thunder – Quick Kick appears)
600-16 Synthoid Conspiracy, Part 1 *** (Rock N’ Roll, Mutt & Junkyard)
600-17 Synthoid Conspiracy, Part 2 *** (Mutt & Junkyard, Rock N’ Roll, Breaker – Quick Kick)
600-18 Spell of the Siren (Cover-Girl, Deep-Six, Torpedo)
600-19 Twenty Questions *** (Shipwreck, Cover-Girl, Spirit, Gung Ho)
600-20 The Gamesmaster **
600-21 The Greenhouse Effect * (Barbecue, Wild Bill, Alpine, Bazooka, Airtight)
600-22 The Viper is Coming * (Barbecue)
600-23 The Funhouse **** (Gung Ho, Zap)
600-24 Where the Reptiles Roam
600-25 Lasers in the Night **
600-26 The Germ ***
600-27 Worlds Without End, Part 1 *****
600-28 Captives of Cobra, Part 1
600-29 Bazooka Saw a Sea Serpent
600-30 The Traitor, Part 1 *****
600-31 Cobra Quake
600-32 Excalibur **
600-33 Cobra CLAWS Are Coming to Town **
600-34 Worlds Without End, Part 2 *****
600-35 Eau De Cobra ****
600-36 Captives of Cobra, Part 2
600-37 The Pyramid of Darkness, Part 1 – The Further Adventures of G.I. Joe *
600-38 The Pyramid of Darkness, Part 2 – Rendezvous in the City of the Dead *
600-39 The Pyramid of Darkness, Part 3 – Three Cubes to Darkness *
600-40 The Pyramid of Darkness, Part 4 – Chaos in the Sea of Lost Souls
600-41 The Pyramid of Darkness, Part 5 – Knotting Cobra’s Coils
600-42 An Eye for an Eye
600-47 The Gods Below
600-43 Primordial Plot
600-44 Flint’s Vacation ****
600-45 Hearts and Cannons
600-46 The Traitor, Part 2 *****
600-48 Memories of Mara ****
600-49 The Wrong Stuff ****
600-50 Last Hour to Doomsday (Season 2 episode)
600-51 The Pit of Vipers
600-52 The Invaders
600-53 Computer Complications (Season 2 episode)
600-54 Sink the Montana (Season 2 episode)
600-55 Cold Slither ****
600-56 The Great Alaskan Land Rush
600-57 Skeletons in the Closet ****
600-58 There’s No Place Like Springfield, Part 1 *****+
600-59 There’s No Place Like Springfield, Part 2 *****+

Season 2
600-60 Let’s Play Soldier
600-61 Cobrathon
600-62 The Million Dollar Medic
600-63 The Rotten Egg
600-64 Once Upon a Joe
600-65 Glamour Girls
600-66 Iceberg Goes South
600-67 The Spy Who Rooked Me
600-68 Grey Hairs and Growing Pains
600-69 My Brother’s Keeper
600-70 My Favorite Things
600-71 Raise the Flagg
600-72 G.I. Joe and the Golden Fleece
600-73 Arise Serpentor, Arise! – Part I
600-74 Arise Serpentor, Arise! – Part II
600-75 Arise Serpentor, Arise! – Part III
600-76 Arise Serpentor, Arise! – Part IV
600-77 Arise Serpentor, Arise! – Part V
600-78 The Most Dangerous Things in the World
600-79 Ninja Holiday
600-80 Nightmare Assault
600-81 Joe’s Night Out
600-82 Second Hand Emotions
600-83 Not a Ghost of a Chance
600-84 Sins of Our Fathers
600-85 In the Presence of Mine Enemies
600-86 Into Your Tent I Will Silently Creep