Season 3

G.I. Joe is acting as the Peace Corps helping a poor village, when they met journalist/cameraman Leonard Michaels aka Scoop who joins the Joes. Cobra attacks a monastery to get the secret to the Dragonfire, a mysterious energy in the earth. Destro dumps the Baroness for Zarana, so Baroness plots with Gnawgahyde to return Cobra Commander to human form to get revenge. Scoop turns out to be a Crimson Guard commander spying on GI Joe...

Cobra has a map showing the locations of Dragonfire around the world, and the Joes and Cobra battle over one of the locations in a mountain. Baroness and Gnawgahyde use the Dragonfire to DNA convert Cobra Commander back into human form. The Joes manage to get inside the mountain base, but are flooded out...

Next location is a jungle temple in South America, and there's three factions: Serpentor, the Joes, and Cobra Commander. Scoop finds out he was tricked into joining Cobra and turns against them. But the Joes discover he's a Cobra. Cobra Commander uses the Dragonfire to turn monkeys in Ape Warriors that attack the Joes...

Scoop returns to Cobra to try to defeat them. Gnawgahyde steals a Conquests and blasts the Joes. Cobra Commander starts fusing animals with vehicles and creates Python Patrol. Serpentor is defeated and fused with Gnogahide's pet iguana. The Joes return to base while Low Light stays behind. Destro dumps Zarana for the Baroness...

The final location is a mesa. Cobra links all of the Dragonfire bases together through their satellite to create an energy weapon and to supercharge their vehicles with the Dragonfire energy. Finally the Joes have their own Dragonfire after Freedom finds a Native American man who knows how to active it. Scoops sends the Joes the frequency to disable Cobra's Dragonfire and causes a chain reaction that destroys all of Cobra's Dragonfire bases.

Cobra Commander threatens to unleash a deadly mind numbing gas on the world unless they surrender to Cobra...

Night Creeper Leader is hit on the head during a battle with the Joes in Egypt and begins to believe he is the reincarnated Pharoah and attempts to take over Egypt...

Metal Heads Grandmother comes to visit, who believes he is the leader of Cobra, much to Cobra Commanders disgust...

The Joes are on vacation at Volcania, also known as 'Club Joe', also on the Island of Volcania is General Hawk, who has been reassigned because his superiors believe he is too old. Cobra launches an attack on Volcania and assumes control of the Island, Destro has created new weaponry which Cobra Commander threatens the world with. When they do not meet his demands, Cobra Commander becomes angered and fires on the California River bridge...

The United Nations do not believe Cobra Commander really destroyed the bridge, and send a fleet to Volcania. General Hawk rescues the Joes and they attack the Cobra Command centre hidden within the Volcano, the command centre is destroyed and takes Destros space gun weapon with it. Cobra Commander and his troops pursue the Joes until reinforcements and the UN fleet arrives, allowing the Joes victory once more.

Cobra plans to destroy the Ozone layer and have people buy Cobra Commanders deadly new sun tan lotion...

The Joes play a football match against Cobra, with Sgt.Slaughter as the ball...

G.I. Joe/Oktober Guard team up with Rampart and Cpt. Krimov to work on a space satellite while Sgt. Slaughter, Sub-Zero and Stretcher monitoring their movements, but Cobra wants it for themselves which led to the capturing of the satellite and the 2 Joes. it up to sub-zero and Stretcher to save them while the Sarge back them up with the troops against cobra attacks.

Cobra Commander disguises himself as a new superhero named Serpent Man in an effort to humiliate G.I Joe...

When G.I Joe are told they are exceeding government funding they have to report to The Battle World proving grounds to learn how to fight cost efficently under the supervision of Dr.Carday who is secretly Zarana in disguise. Meanwhile Cobra Commander plans to steal a new weapon named 'The General'...

Low Light faces supernatural beings, while Night Creeper Leader plans to regain favour with Cobra Commander...

Cobra Commander tries to make a break into the world of stand up comedy by impersonating a famous comedian while planning a trap for the Joes...

Ambush finds his lost love Evy, only to find she has now joined Cobra...

Pathfinder, Ambush and Topside infiltrate a Cobra training camp when Cobra suddenly seems to know their every move...

Cobra Commander, Destro and Metal Head allow themselves to be imprisoned in Alcatraz so that they can gain access to a highly powerful weapon on the Comstock Lode submarine outside of the prison...

The Cobras escape from Alcatraz and prepare to use their new weapon to take over the world, now GI Joe has to stop their most devious scheme yet...

Duke is captured by Gnawgahyde who uses a device called the Mind Mangler to try and break into Dukes brain, but a girl named Megan helps Duke escape, little does he know that Megan is really a disguised Zarana planning to steal GI Joes secrets...

Destro creates a super computer named BIOK, which infiltrates every computer system in the world, but soon BIOK turns on them and has plans of its own to take over the world...

After a battle, Cobra Commander and Pathfinder become lost in the Jungle with a enraged Gorilla in pursuit...