||"The Further Adventures of G.I. Joe"
||Zartan and the Dreadnoks capture Space Station Delta as phase one of Cobra's Pyramid of Darkness.
||"Rendezvous in the City of the Dead"
||Shipwreck and Snake-Eyes travel underneath Enterprise City with secret control cubes while G.I. Joe plans to stop Destro from activating the first cube at the Devil's Playground.
||"Three Cubes to Darkness"
||Tomax is captured by G.I. Joe, causing Xamot to plan on rescuing his brother 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.
||"Chaos in the Sea of Lost Souls"
||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.
||"Knotting Cobra's Coils"
||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.
||"Countdown for Zartan"
||Zartan is sent to blow up the Worldwide Defense Center, but G.I. Joe captures and places him in the Defense Center's prison.
||"Red Rocket's Glare"
||Roadblock's aunt and uncle run a fast food place called Red Rocket owned by Extensive Enterprises. 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 warheads.
||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 Stops the World"
||Cobra uses a cloaking device to make oil tankers disappear so they can detonate by remote, unless G.I. Joe can stop the bombings.
||Dr. Shakur, a scientist who invented the Vulcan Machine, is captured by Cobra. G.I. Joe must head into Cobra's base, rescue Dr. Shakur and stop Cobra from carrying out their mission.
||Cobra invents a special weapon called Hi-Freq to take control of all animals, including Mutt's dog Junkyard. G.I. Joe has to stop Cobra's Hi-Freq and save every animal in the world.
||Five 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 "Twenty Questions".
||"The Greenhouse Effect"
||A top secret rocket fuel is stolen and accidentally stored in a greenhouse. The plants grow immensely, giving Destro a plan to seed the world with mutated vegetables to crush G.I. Joe.
||"Haul Down the Heavens"
||Cobra creates a weapon called the Ion Attractor that can pull down the Aurora Borealis and flood the world.
||"The Synthoid Conspiracy (Part I)"
||Zartan makes constructs called Synthoids, artificial beings loyal only to Cobra. Cobra makes Synthoids of Admiral Ledger, Col. Sharp, Gen. Franks, Gen. Howe, and Duke to cut off G.I. Joe's resources and undermine morale.
||"The Synthoid Conspiracy (Part II)"
||Destro helps G.I. Joe defeat Cobra Commander and Zartan to regain G.I. Joe's resources.
||"The Phantom Brigade"
||Cobra Commander and the Baroness hire a Gypsy to summon three ghosts; a Centurion warrior, a Mongolian Amazon and a WWI American ace, to destroy G.I. Joe. Baroness informs the Joes to locate a Roman coin, wedding ring and heart-shaped locket from Cobra Commander, and then bury the items to make the ghosts disappear.
||"Lights! Camera! Cobra!"
||Cobra Commander's personal Firebat with a homing signal was located at a Hollywood studio for a filming of "The G.I. Joe Story". Cobra hires Zartan and the Dreadnoks to recapture the Firebat before G.I. Joe can discover it and use the homing device to attack Cobra headquarters.
||A sleazy candidate hires Cobra to cause trouble for his opponent.
||"Money to Burn"
||Cobra invents a molecular degenerator to disrupt all U.S. currency, allowing them to mint their own money.
||"Operation Mind Menace"
||Cobra captures people with telekinetic abilities in order to exploit their powers to rule the world.
||"Battle for the Train of Gold"
||Cobra steals all the gold bars from Fort Knox and loads it inside a bullet train. G.I. Joe plans on stopping the Cobra Bullet before it reaches the coast.
||Cobra attacks a Sheik's oil supply.
||"Where the Reptiles Roam"
||Wild Bill and a few Joes head to Texas to investigate a farm Cobra bought, near the solar panels.
||A twisted tycoon on a private island orders his automaton army to capture Joes and Cobra, causing both sides to come together to fight the gamesmaster.
||"Lasers in the Night"
||The Baroness spies on the Joes to gain access to the laser guidance system for Cobra Commander, just as Quick Kick meets a girl named Amber who dreams of being a Joe.
||Cobra's in-fighting cause a strong bacterium and growth serum to form a living germ that consumes everything in its path.
||"The Viper is Coming"
||Barbecue gets phone calls from a man who calls himself "The Viper."
||"Spell of the Siren"
||The Baroness discovers a conch shell containing the song of the Sirens, and uses its power to hypnotize the Joe and Cobra men.
||Cobra heads to Japan to cause an earthquake that will destroy Tokyo unless G.I. Joe can stop their plans.
||"Captives of Cobra (Part I)"
||Baroness hires Storm Shadow to sneak into the Department of Defense to capture families of the Joes in order to retrieve radioactive crystals.
||"Captives of Cobra (Part II)"
||Baroness plans on destroying the crystals and the Joes before they can retaliate.
||"Bazooka Saw a Sea Serpent"
||While camping out, Bazooka sees a Cobra flight pod eaten by a sea serpent. The sea serpent is in reality a Cobra submarine planning to steal everything the serpent devours.
||As G.I. Joe sets up a radar tracking station in England, Storm Shadow finds the legendary sword Excalibur, using its strength to attack G.I. Joe and destroy the tracking station.
||"Worlds Without End (Part I)"
||Cobra invents a matter transformer, but the Joes steal the machine's blueprints. The machine sends the Joes into an alternate universe where Cobra rules the world.
||"Worlds Without End (Part II)"
||While stuck in the alternate world, the Joes find an unlikely ally in the Baroness. She helps rescue the Joes and sends them home.
||"Eau De Cobra"
||Cobra concocts a love potion for Baroness to make a wealthy shipping tycoon fall in love with her.
||"Cobra Claws Are Coming to Town"
||Cobra rewires the G.I. Joe equipment, planning on attacking Keystone City to have people believe G.I. Joe has turned treacherous.
||"An Eye for an Eye"
||The Joes accidentally set a cabin on fire and its owner, Charlie Fairmont, demands redemption.
||"The Gods Below"
||Cobra heads for Egypt to steal the treasure of Osiris. G.I. Joe find themselves facing Osiris and the Egyptian gods while Cobra faces Set, the Egyptian god of evil.
||Cobra kidnaps a biologist to have him recreate dinosaurs in order to rule the world.
||Flint visits family in Pleasant Cove, a town secretly owned by Cobra.
||"Hearts and Cannons"
||A young prince named Jabal plans on avenging the capture of his people by Cobra.
||"Memories of Mara"
||G.I. Joe go underwater to find a nuclear submarine called the Nerka, to rescue a crew held captive by Cobra. Helping in the search is Mara, a girl genetically modified by Cobra to be an underwater soldier.
||"The Traitor (Part I)"
||G.I. Joe chemists make an armor impenetrable to laser fire and missiles, and Dusty secretly informs Cobra about the armor.
||"The Traitor (Part II)"
||G.I. Joe revamp security and launch a full scale assault against Cobra.
||"The Pit of Vipers"
||Col. Sharp buys a computer program called Watchdog to be the computer commanding officer for G.I. Joe, until they discover later it was owned by Cobra.
||"The Wrong Stuff"
||Cobra captures satellites to create their own television network. G.I. Joe must head into space and destroy the space station before Cobra's propaganda infects everyone in the world.
||Cobra devises a plot to take control of Washington, D.C. and Moscow with the aid of UFO's, causing suspicion and paranoia between the U.S.A. and the Soviet Union. The Joes and the Oktober Guard reluctantly join forces to stop Cobra.
||Zartan and the Dreadnoks form a band as part of a Cobra subliminal message to take control of the population.
||"The Great Alaskan Land Rush"
||G.I. Joe and the Oktober Guard need to locate the real Seal of Alaska before Cobra takes control of Alaska and its resources.
||"Skeletons in the Closet"
||Lady Jaye inherits a castle in Scotland, which turns out to be Castle Destro. G.I. Joe heads to Scotland to rescue Lady Jaye.
||"There's No Place Like Springfield (Part I)"
||On an island, Lady Jaye and Shipwreck rescue Professor Mulaney who remembers a secret formula to turn water into a bomb. Shipwreck passes out trying to escape after a Cobra assault and wakes up in a place called Springfield, with Mara as his wife and daughter named Alfea.
||"There's No Place Like Springfield (Part II)"
||Shipwreck calls the Joes to Temple Alpha, Springfield's true area, and plan to take down Cobra once and for all.
||"Arise, Serpentor, Arise! (Part 1)"
||The Joes embark on a mini-remedial recruit training and intercept and destroy a Cobra Night Raven, retrieving a Cobra message pod. The Joes find a letter detailing the Dreadnok's mission to break into tombs of history's greatest leaders and conquerors.
||"Arise, Serpentor, Arise! (Part 2)"
||The Joes set off to protect the tombs. Zarana tricks the Joes into helping local villagers and leave the tomb of the Egyptian General undefended. In Paris, Cobra troops arrive by submarine, and the Crimson Twins get into Napoleon's tomb. The Joes are unable to stop Cobra from getting Montezuma's DNA.
||"Arise, Serpentor, Arise! (Part 3)"
||Duke and his group defends Genghis Khan's tomb while Shipwreck's group defends Alexander the Great's underwater tomb. The Joes think Cobra is building an army of super cloned soldiers
||"Arise, Serpentor, Arise! (Part 4)"
||The Joes plan an attack on Cobra Island and suddenly find out Cobra's true plan for DNA gathering: to create the Cobra Emperor known as Serpentor.
||"Arise, Serpentor, Arise! (Part 5)"
||The Joes use Lifeline to distract the Cobras and sneak into the Terror Drome to rescue Sarge from Serpentor. After the rescue, Serpentor launches a full-scale assault on Washington, D.C., leaving the Joes to desperately stop Cobra before the world is doomed.
||"Last Hour to Doomsday"
||Cobra demands the U.S. to submit or they will use a giant vortex to destroy the East Coast.
||A space probe containing anti-matter crashes into the ocean and both Joes and Cobra try to retrieve it. Cobra steals the probe, using the anti-matter to power their aircraft, which then crashes into the USS Flagg.
||"Sink the Montana!"
||The Joes are at the decommissioning ceremony for a battleship, the USS Montana, when Cobra and the ship's former captain, Admiral Lattimer, try to foil the plans.
||"Let's Play Soldier"
||The Joes raid a village in southeast Asia to prevent villagers from collecting tree sap for Cobra.
||"Once Upon a Joe"
||Cobra Stratovipers attempt to steal the MacGuffin Device but are stopped by G.I. Joe.
||"The Million Dollar Medic"
||In the Joe/Cobra battle in the Caribbean, a civilian yacht is sunk, but the Joes save the day. The heiress, Bree, falls for Lifeline who helped her recover.
||Cobra pirates airwaves and stages a telethon to raise funds for criminals and terrorists in order to delete all known terrorist activities from Interpol's database.
||"The Rotten Egg"
||Leatherneck attends graduation ceremonies at a new academy and discovers it run by dishonorably discharged soldier Buck McCann, now leader of Cobra's own Marine Corps.
||Madame Vail agrees to sell her youth transference machine in return for kidnapping the world's top models, who's youth and beauty will be transferred to the machine's user.
||"Iceberg Goes South"
||The Joes are in an Arctic region training and testing new equipment.
||"The Spy Who Rooked Me"
||The Joes must work alongside English secret agent Matthew Burke to stop Cobra from obtaining a paralyzing gas.
||"Grey Hairs and Growing Pains"
||Cobra develops technology for rapid aging and deaging, turning three of the Joes into children and three into eldery people.
||"My Brother's Keeper"
||Sgt. Slaughter accompanies Sci-Fi to a science fiction convention, where Dr. Mindbender recruits a handicapped scientist to repair his latest weapon.
||"My Favorite Things"
||Serpentor collects artifacts from his former lives to gain power.
||"Raise the Flagg!"
||G.I. Joe and Cobra mount separate salvage operations to recover the sunken USS Flagg, only to find a former Cobra agent named Lakar and reprogrammed BATs occupy the Flagg and renamed it Lakar City.
||Cobra Commander plots to find an assassin to eliminate Serpentor.
||"G.I. Joe and the Golden Fleece"
||Joes and Cobras race to capture a golden coil dropped from a UFO, and the device sends them back in time to ancient Greece, where they are mistaken for deities.
||"The Most Dangerous Thing in the World"
||While Hawk was attending a NATO meeting, Cobra hacks into the Defense Department and upgrades Shipwreck, Dial-Tone and Lifeline to the rank of Colonel.
||Dr. Mindbender creates a device allowing him to affect the dreams of the Joes, and Cobra brings elements of their dreams into their attacks.
||"Second Hand Emotions"
||Dr. Mindbender constructs a musical instrument to influence the Joes' emotions.
||"Joe's Night Out"
||Leatherneck, Wet Suit, and Dial-Tone visit a new nightclub which is a Cobra rocket in disguise, sending the trio to space.
||"Not a Ghost of a Chance"
||Cobra is suspected of shooting down an experimental stealth plane.
||"Sins of Our Fathers"
||Dial-Tone is dismissed from the Joe team and ends up helping Cobra Commander raise a monster from the ruins of Castle Destro in order to destroy Serpentor.
||"In the Presence of Mine Enemies"
||When Slip-Stream is shot down by a female Strato-Viper near an abandoned Cobra laboratory, both hunt each other down.
||"Into Your Tent I Will Silently Creep"
||Cross-Country tries to track down the theft of Joes' personal items and finds them being taken by robots. Among them was a game program Mainframe was working on simulating battle tactics.
||"United We Stand"
||Ambush and Pathfinder have to work together or perish!
||"Revenge of the Pharaohs"
||Night Creeper Leader thinks he is an Ancient Pharaoh and has his sights set on Lady Jaye!
||Metal-Head's granny comes to visit and thinks Cobra is the good guys!
||"Victory at Volcania I"
||Cobra attacks while the Joes are resting, and General Hawk questions his usefulness to G.I. Joe.
||"Victory at Volcania II"
||Cobra has the Joes on the run, can Hawk rally for a victory?
||"The Nozone Conspiracy"
||Cobra decides to blackmail humanity into protecting itself from the Ozone!
||Sgt. Slaughter is kidnapped and its up to Grid-Iron to save him.
||GI Joe/Oktober Guard team up to work on a space satellite, but Cobra wants it for themselves!
||"Injustice and the Cobra Way"
||There is a new Hero in the world, will G.I. Joe be forgotten?
||G.I. Joe's massive expenses come under review by the Government.
||"Night of the Creepers"
||Lowlight and Scoop track Night Creeper Leader into an ancient city.
||General Hawk becomes angered at the lax nature of his troops and their infatuation with a movie star.
||"I Found you Evy"
||Ambush reveals a story from his past, about the only person who has ever been able to find him....a Female Viper named Evy!
||"An Office and a Viperman"
||Someone from G.I. Joe is leaking sensitive information, 3 Joes infiltrate Cobra to find the culprit.
||"D-Day at Alcatraz I"
||Cobra is finally arrested and put in prison...but is there more to their capture?
||"D-Day at Alcatraz II"
||Cobra has deceived the Joes and has captured the Comstock load, can Grid-Iron defeat the odds and win the day?
||"The Mind Mangler"
||Duke is captured by the Mind Mangler to reveal the location of the Joes base, can Sky Patrol save him?
||Super Computer BIOK decides to attack the Joes using their own weapons, can Sky Patrol defeat it?
||"Stuck on You"
||Pathfinder and Cobra Commander attempt to escape a Jungle safely when both crash during a battle.
||When sensitive information is leaked, can Mercer convince the Joes he is not a traitor?
||Cobra Commander kidnaps the Queen of England, can Duke save her in time?
||"A is for Android"
||General Hawk has a clone, and the Joes have to figure out which Hawk is real!
||"El Dorado: The Lost City of Gold"
||Grunt discovers the Lost City of Gold, will Cobra soon follow!
||"Long Live Rock N Roll I"
||Cobra creates a sonic attack that can cripple the city, G.I. Joe has to stop them!
||"Long Live Rock N Roll II"
||Rock N Roll and Snake Eyes race to save the city against Cobra's sonic attacks
||"The Sludge Factor I"
||Cobra attacks a chemical plant and causes an environmental disaster
||"The Sludge Factor II"
||Cesspool who was created during the attack has both G.I. Joe and Cobra at his mercy
||"Messenger from the Deep"
||G.I. Joe discovers an ancient underwater city...but Cobra is hot on their heels!
||Cesspool has a new plan to bring humanity to his feet...by turning into bugs!
||"The Greatest Evil I"
||The Headman has the city in his grips with drugs, and he gets Falcon hooked!
||"The Greatest Evil II"
||G.I. Joe and Cobra have teamed up take down the Headman, can they rescue Falcon in time?
||"Shadow of a Doubt"
||Cobra Commander is imprisoned and Storm Shadow helps him escape, has Storm Shadow become a traitor?
||Cobra's computers are infiltrated by a young computer hacker who thinks its a video game
||Snake Eyes and Storm Shadow race against the clock to beat Night Creeper Leader to a magical sword
||Cobra buys an amusement park, has Cobra turned good?
||Cobra Commander wants the perfect soldier, can Mercer stop his evil plan?
||"Metal Heads Reunion"
||There is a High School Reunion for Capt Grid-Iron and Metal-Head.But Metal-Head wants to make sure he is remembered!
||Recap episode detailing events of Season 1(a little part of season 1) & Season 2 and the life of a G.I. Joe, as hosted by Hawk.
||"The Legend of Metal Head"
||Recap episode detailing Metal-Head's time in the DIC series.