The Eliminator
E1
Overkill recieves an upgrade and becomes The Eliminator, and sets out to destroy the Joes.
Chunnel
E2
At the unveiling of a new tunnel between England and France, Cobra Commander kidnaps the Queen of England and steals the crown jewels, proclaiming himself King...
A is for Android
E3
Cobra replaces General Hawk with an android replica...
El Dorado, The Lost City Of Gold
E4
Grunt and Cobra Commander by search for El Dorado, The Lost City of Gold.
Long Live Rock & Roll (1)
E5
Cobra plans to destroy New York city by using subliminal messages in Rock and Roll music.
Long Live Rock & Roll (2)
E6
The Joes race to stop Cobras Rock and Roll scheme...
The Sludge Factor (1)
E7
Cobra joins forces with the evil Cesspool to pollute the worlds food supplies, and the Joes form the Eco Warriors to combat this new threat...
The Sludge Factor (2)
E8
The Eco Warriors race to stop Cobra Commander and Cesspool from taking control of the world from their volcano base...
Messenger from the Deep
E9
Cobra Commander believes a hidden city under the sea will make him rich, but both the Joes and Cobra find out it holds a more dangerous secret...
Infested Island
E10
Cesspool and Cobra Commander attempt to take over the world with giant insects.
The Greatest Evil (1)
E11
Cobra and GI. Joe team up to fight a Drug dealer...
The Greatest Evil (2)
E12
While Duke and his younger brother Falcon have a conflict of their own, Cobra Commander plans to steal the Drug Lord Headmans money reserves.
The Sword
E13
Storm Shadow, Snake Eyes and Night Creeper leader all race for posession of the mythical sword of destiny...
Keyboard Warriors
E14
Destro creates a new computer system named the ASP which can control Cobra weapons around the world.
Shadow of a Doubt
E15
Cobra Commander attempts to lure Storm Shadow back into Cobra...
Cobra World
E16
Cobra Commander tries to convince the world he has gone straight and opens his own theme park...
Kindergarten Commandos
E17
Cobra takes control of a school in the hope of training new Cobra recruits from a young age.
Metal Head's Reunion
E18
Metal-Head goes to his high school reunion in an effort to get a secret armor formula for Cobra...
Basic Training
E19
In a clip show, General Hawk advises the audience what it takes to become a GI.Joe.
The Legend of Metal Head
E20
In another clip show episode, Metal Head relates his time in Cobra to the audience.