1The Pyramid of Darkness: Part 1 - The Further Adventures of G.I. Joe
2The Pyramid of Darkness: Part 2 - Rendezvous in the City of the Dead
3The Pyramid of Darkness: Part 3 - Three Cubes to Darkness
4The Pyramid of Darkness: Part 4 - Chaos in the Sea of Lost Souls
5The Pyramid of Darkness: Part 5 - Knotting Cobra's Coils
7Red Rocket's Glare
Roadblock goes to visit his relatives who have put their life savings into a diner. They're having troubles with bikers. After a few inquiries, Roadblock finds out that ALL of the franchises have been bought by the parent company, except for Roadblock's family, and there's something strange with the parent company and what they've done with the diner's they've bought back.
11Cobra's Creatures
COBRA gains new allies: the animal kingdom, through "High Freq", an animal mind control device. In a race against time, the Joes must stop "High Freq" before Mutt loses the fight against Junkyard, his best friend who is now his worst enemy.
16Synthoid Conspiracy: Part 1
17Synthoid Conspiracy: Part 2
18The Phantom Brigade
Through gypsy magic, Cobra Commander gains 3 new forces in the fight against G.I. Joe: a WW1 pilot, a Mongolian princess, and a Roman centurion, which gives the Joes a new dilemma: How do you stop the enemy when they're not flesh and blood?
23Battle for the Train of Gold
25Where the Reptiles Roam
29The Viper Is Coming
A mysterious person calling himself the Viper is leaving cryptic messages on one of the Joes answering machines. When the Joes investigate the messages, they encounter Cobra. The Joes and Cobra want to find out who is this mysterious Viper and how he knows so much about Cobra.
32Captives of Cobra: Part 1
33Captives of Cobra: Part 2
36Worlds Without End: Part 1
37Worlds Without End: Part 2
A small group of Joes are on an alternate world where the Joes have lost the war. They find an unexpected ally, and that Cobra has dissension within its ranks. While they try to find a way back to their own reality, some realize why the fight must continue, and where they can do the most good.
38Eau de Cobra
Cobra finds a tablet with a perfume used by Cleopatra. The scent makes men fall for which ever female wears it. The Baroness uses the formula to woo a rich single bachelor. Flint tries to stop her, but he's affected by the perfume as well. It's up to Lady Jay to stop her, she'll get some help from an unexpected ally.
39Cobra Claws Are Coming to Town
47The Traitor: Part 2
Duke's been injured. The traitor has been discovered, now the former Joe is working for Cobra. The Joes must capture their former comrade, but he knows their methods, and can anticipate their moves. The Joes are soon captured, but an unexpected turn will reveal what's really going on.
51Cold Slither
Cobra's latest scheme is to form a band, Cold Slither. Their music is filled with subliminal messages, that draws whomever listens to their concert. Then they can hold them for ransom. Shipwreck and a few other Joes, listen and get taken as well.
52The Great Alaskan Land Rush
When the U.S. bought Alaska from Russia, they were supposed to get the Seal of Alaska. But the ship carrying the seal was lost at sea. Cobra has found the seal, terms of the agreement specified that the possessor of the seal owned Alaska. The Joes must get the seal from Cobra, but they're not the only interested party who's after the seal.
53Skeletons in the Closet
54There's No Place Like Springfield: Part 1
Shipwreck and Lady Jay go on a mission to pick up a scientist who claims to have developed a new weapon. When they find him, he implants the secret formula into Shipwreck's brain, which can only be released by a secret code word he gives to Lady Jay. As they try to evade Cobra, Shipwreck is knocked unconscious. When he wakes up it's several years later, the Joes have defeated Cobra, and he's married to Mara. He tries to remember/figure out what happened during the missing years.
55There's No Place Like Springfield: Part 2
11The Million Dollar Medic
14Glamour Girls
Cobra sits in a room watching a simulation of a woman going through a beauty transfer. The first woman is old and decrepit and the other woman is young and beautiful. The young woman begs to be let out of the machine but to no avail as her face is left with no eyes or mouth. Then Madame Vail makes Cobra an offer to get her longevity secrets for a price. Cobra must provide Madam Vail with an abundance of young women with which she can keep her operation going. Dr Mindbender calls it "Operation: High Fashion." Meanwhile Low-Light and Dial-Tone are helping Low-Light's sister Una, and her friend Satin move into their own apartment. Low-Light admits that he doesn't like the neighborhood with all of the crazies in here. Una tells Low-Light that she can look after herself. Satin then reminds Low-Light that she lived with him right? Then Una and Satin receive a letter from Glamour Girls magazine, a high fashion magazine, to come to a photo shoot. Again Low-Light is suspicious when he reads the letter but Una and Satin insist on doing the photo shoot.
17Grey Hairs and Growing Pains
The investigation into the theft of a youth formula leads Flint, Lady Jaye, and four other Joes to the COBRA owned Ageless Care spa, where they find they might have some trouble stopping COBRA after being turned into young kids and old men.
22G.I.Joe and the Golden Fleece
The Joes get a new battleground to fight COBRA: ancient Greece, when a stray laser blast hits a mysterious golden coil, sending the Joes and COBRA back in time, where the Joes must find a way to return to our time, without changing history.
23The Most Dangerous Thing in the World
Cobra hacks into the the Defense Department, and promotes Life Line, Dial Tone, and Shipwreck to full Colonels. With General Hawk away at a conference, these three are now in charge, which causes major issues when Cobra launches an assault.
24Nightmare Assault
Dr. Mindbender creates the Somnia machine, a device which he plans to cause disarray in a number of Joes by entering their dreams and change them into nightmares, hoping to affect their morale and mental stability during their waking hours.
27Not a Ghost of a Chance
29In the Presence of Mine Enemies
30Into Your Tent I Will Silently Creep