Cobra kidnaps scientist Dr. Shakur in order to harness the energy of Earth's core and cause volcanic eruptions, but the Joes work through a number of traps to raid Cobra's jungle base and destroy Cobra's newest weapon.

Mutt, Junkyard, & Ripcord are kidnapped by Cobra, so that the evil scientist, Dr. Lucifer, can test his new invention, High Freq, a device which controls the minds of animals and insects, on Junkyard. Cobra use it to gain control of an army of animals to take over the world, and send Junkyard hunting after Mutt. In exchange for High Freq, Cobra agrees to break Dr. Lucifer's love, Dr. Attilla, out of jail. GI Joe learns of this, and has Scarlett pose as Attilla, but it's obvious to Lucifer she is not Attilla, and Scarlett is captured. Snake-Eyes and Spirit come to the rescue, using Timber and Freedom to sneak into Cobra's jungle castle and rescue Ripcord and Scarlet, and stop High Freq.

Flint, Dusty, Bazooka, Alpine, and others have to break into a temple to stop Cobra from its next plan to take over the world. When the temple turns out to be a fun house with obstacles of death, the Joes have to find their way to Cobra Commander and save the day!

Investigative reporter Hector Ramirez believes that Cobra is not a real threat and that G.I. Joe is a drain on taxpayers' money. But Shipwreck takes him on an unauthorized mission into Cobra territory to prove their danger.

A Crimson Guard steals a container filled with experimental rocket fuel, causing plants to grow to gargantuan sizes. Destro convinces Cobra Commander that the plants could be used in combat. Harvey 15 Bullock 6

The Joes travel to the arctic regions at the top of the world in order to stop Cobra from using the Aurora Borealis to melt the ice and flood coastal cities around the world.

Cobra attempts to cripple the Joes from within by replacing leaders and committee members with artificial beings known as synthoids. The synthoids cut G. I. Joe's budget and eventually order the team to disband.

When Destro discovers a synthoid of himself, he aids the Joes in defeating Cobra's synthoid plot.

Cobra Commander recruits an elderly Gypsy woman to use three small artifacts, which allow them to command three ghosts to attack the Joes. The Baroness and a phantom World War One pilot help the Joes recover the artifacts.

Movie producer wants the real G.I. Joes to star in his movie about them after finding actors to be too unrealistic.

Cobra backs a candidate for mayor and uses street thugs to intimidate voters and drum up public sympathy for Cobra's would-be mayor. The gang turns on Cobra when a brother of one of the youths is nearly burned in a fire.

Cobra creates a machine that destroys all the money in the country leaving all its citizens vitually penniless.

Flash, Airborne, and several other Joes discover that Cobra has amplified the psionic powers of some civilians for use as living weapons; one of the captives is Airborne's telekinetic brother.

Cobra steals the gold stored at Fort Knox and begins moving it out with a bullet train. When the Joes' equipment is destroyed in a surprise attack, they must use horses to stop the train.

Cobra develops a powerful sonic weapon and begins testing it on a country in the Middle East. An Arabian prince assists the Joes.

Cobra purchases a dude ranch through one of its dummy corporations, intending to control a nearby solar power station. G. I. Joe travels to the ranch to flush out the Cobras.

A bored game player decides to have members of both G.I.Joe and Cobra become part of his newest and most dangerous game where they are the victims.

Quick Kick's girlfriend Amber breaks into G.I. Joe Headquarters with the intent of joining the team, and Cobra Commander steals a prototype laser device to carve his likeness on the moon.

A Cobra spy steals a deadly bacteria along with an experimental growth serum and accidently creates a living, growing and monstrous terror. G.I. Joe must use an orchard of apples to destroy it.

The ""viper"" is making phone calls leading the Joes to stopping all of Cobra's plans of domination. But one question remains, who is the ""viper""?!

The Baroness discovers a conch shell whose song hypnotizes men. She uses the shell to seize control of Cobra and capture most of the Joes. One of the Crimson Twins aids Scarlett, Lady Jaye, and Cover Girl in rescuing their companions.

Cobra decides to test a new earthquake-causing weapon to disrupt a Japan peace conference. It is up to Quick Kick, Bazooka, and their trainees to stop Cobra.

Cobra kidnaps relatives of the Joe team and uses mind-control technology to turn the Joes' families against them. Their goal is to steal highly unstable explosive crystals.

As the Joes and their families are endangered by the highly explosive crystals, Scarlett and others try to disable the mind-control center.

Cobra unleashes an enormous mechanical sea-serpent that devours any seacraft it comes across, enslaves its captives and grows biggers the more it eats.