Zartan and the Dreadnoks capture Space Station Delta and destroy G.I. Joe headquarters as phase one of Cobra's "Pyramid of Darkness", a plan for Cobra Commander to deprive the world of electricity.

As G.I. Joe sets up their base of operations on the U.S.S. Flagg, on Delta Space Station, Dusty and Mutt warn the team about Cobra's plan to plant cubes at strategic locations in order to create the pyramid of darkness. Shipwreck and Snake Eyes travel underneath Enterprise City with secret control cubes, while the rest of the Joes plans to stop Destro from activating the first cube at the "Devil's Playground".

Tomax is captured by G.I. Joe, causing his identical twin brother Xamot to plan on rescuing him before Cobra can activate the final cube in the "Sea of Lost Souls". Shipwreck and Snake Eyes find an ally in a pop singer named "Satin", who helps them escape Cobra's troopers in Enterprise City.

Cobra activates the Pyramid of Darkness, leaving the Joes stranded at sea. The Crimson Twins anticipate Cobra Commander's treachery and signal for the Dreadnoks to relieve Zartan and Cobra Commander of control. Alpine and Bazooka ally with Quick Kick, a stuntman and karate expert from Hollywood.

G.I. Joe regains control of Space Station Delta, and they launch a full-scale assault on Cobra Temple, destroying the control cubes and the Pyramid of Darkness.

Cobra tries to take over a global anti-terrorism conference when they send Zartan to replace an ambassador and blow up the Worldwide Defense Center, but G.I. Joe captures and places him in the Defense Center's prison.

Roadblock's aunt and uncle run a fast food place called Red Rocket owned by Extensive Enterprises, Cobra's business alias. The rocket design hides extremely destructive warheads that Cobra hopes to utilize. G.I. Joe goes on a countrywide search for Red Rocket restaurants with Cobra missiles.

A military satellite crashes into the South Pacific, causing a race between G.I. Joe and Cobra to gain possession of it. A primitive tribe finds it first, claiming it as their god.

Cobra uses a cloaking device to make oil tankers disappear so they can detonate them by remote in an effort to take control of the world's fuel supply, unless G.I. Joe can stop the bombings.

In a plan to attack the world's cities with lava, Dr. Shakur, a scientist who invented the Vulcan Machine, is captured by Cobra. G.I. Joe must head into Cobra's jungle base, rescue the doctor and stop Cobra from carrying out their mission before these cities literally become "hotspots".

Cobra uses a special weapon called "Hi-Freq", a mind control device that takes over all animals in the animal kingdom, including Mutt's dog Junkyard. G.I. Joe has to stop Cobra's Hi-Freq device and save every animal in the world, especially Junkyard who isn't man's best friend, but Mutt's worst enemy.

Several scientists have been captured by Cobra and imprisoned in South America, prompting the Joes to rescue them and go through Cobra's booby-trapped "funhouse".

The Joes discover Cobra's plan to invade the Rocky Mountain Chemical Weapons Arsenal to possess explosive gas, all while under scrutiny from Hector Ramirez, host of the television show Twenty Questions.

A top secret nitrogen rocket fuel is stolen from the Joes and is accidentally stored in a greenhouse. The plants grow immensely, giving Destro a plan to seed the world with mutated fruits and vegetables to crush G.I. Joe in this gigantic jungle.

Cobra creates a weapon called the "Ion Attractor" that can pull down the Aurora Borealis to melt the polar icecaps and flood the world. G.I. Joe and a group of scientists must head north to prevent a global disaster.

Zartan makes constructs called synthoids, artificial beings or life forms loyal only to Cobra. Cobra makes Synthoids of Admiral Ledger, Colonel Sharp, General Franks, General Howe, and Duke to cut off G.I. Joe's resources and undermine morale.

The Joes have never seen a worse day: disbanded by the government, fugitives from the military, and betrayed by an impostor in their ranks, this truly is the end of G.I. Joe, that is, unless they accept help from a very unlikely source.

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?

The Joes go to Hollywood when hired as technical advisers on 'The G.I. Joe Story', to add realism to the film. But the studio may get more realism they can handle when there is a Firebat at the studio that COBRA wants back, at any cost.

When Robert Harper's rival in the mayoral race keeps sending gang members to reap havoc and ruin Harper's campaign, the Joes are sent in to restore law and order, but Scarlet and Lady Jaye soon find out things are not what they seem.