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1-85 of 85
- 1985–198622mTV-Y8.2 (80)TV EpisodeShipwreck and Lady Jay go on a mission to pick up a scientist who claims to have developed a new weapon. When they find him, he implants the secret formula into Shipwreck's brain, which can only be released by a secret code word he gives to Lady Jay. As they try to evade Cobra, Shipwreck is knocked unconscious. When he wakes up it's several years later, the Joes have defeated Cobra, and he's married to Mara. He tries to remember/figure out what happened during the missing years.
- Part 2 of 2. Trapped in the alternate Cobra - controlled world, the Joes find an unlikely ally in the Baroness. With her help, Stealer, Clutch and the others search for a way back to their own reality. But Cobra is closing in...
- Some Joes start to have doubts about whether or not the fight with Cobra is doing any real good. Maybe they should just stop fighting. A small group of Joes find themselves in a place where the Joes have apparently lost to Cobra.
- The Joes are reunited with old friends (The Oktober Guard), and face new enemies (The B.A.T.'s and new Dreadnok's) as COBRA commences it's DNA extraction operation for the creation of Serpentor.
- The Joes have their hands full when Serpentor's first action as the Cobra Emperor succeeds, as he takes over Washington, D.C. in this concluding episode of the second season miniseries.
- Dissatisfied with Cobra Commander's leadership, Dr. Mind Bender proposes genetically creating an ideal new leader.
- When Sgt. Slaughter destroys a batch of DNA needed for the creation of Serpentor, Dr. Mindbender is undaunted by the action and makes his decision for the subject for a substitute batch, much to the surprise of COBRA.
- Just as the Joes perfect a new body Armour formula, they find evidence to suggest that one of them is giving their secrets away to Cobra. All the evidence seems to point to a senior Joe agent.
- Cobra tries to undermine a global anti-terrorism conference by sending Zartan to replace an ambassador.
- While infiltrating a COBRA temple to save a group of kidnapped scientists, the Joes find the temple filled with funhouse attractions, designed not to amuse, but to stop the Joes in their tracks, permanently.
- After collecting the DNA needed, Dr. Mindbender begins creating Serpentor, but unknown to Mindbender, Cobra Commander sabotages the experiment, creating a monster. Will this stop Dr. Mindbender from creating the perfect COBRA Emperor?
- While on a Joe mission to locate a downed sub, Shipwreck saves a woman with blue skin named Mara, and soon finds out why she has blue skin: She's what, in old sailor's terms, is called a mermaid, and COBRA wants her back.
- 1985–198622mTV-Y7.6 (73)TV EpisodeShipwreck is still trying to figure out what happened in those past six year, and he's plagued by nightmares. Soon he'll learn the truth.
- 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.
- Cobra Commander has a plan to defeat G.I. Joe without firing a shot: replacing the officials that's over the Joes with Synthoids, an artificial life form. But Cobra Commander has placed another Synthoid in a place no one would ever expect.
- The Joes try to dispose of the highly explosive crystals before COBRA gets their hands on them, while trying to find a way to release their family members from being under the effect of the COBRA brainwashing.
- Complications arise over gaining computer control of subs retrieving a space probe. For the Joes, it's not reprogramming them after using them to fight COBRA subs. And for COBRA, it's because Zarana, in disguise, has fallen for Mainframe!
- While repairing the damage to a orphanage caused during the Joes battle with COBRA over "The McGuffin Device", Shipwreck tells a little girl a simple fairy tale, but little does he know, his story may have the power to help save the day.
- Lady Jaye gets a letter of inheritance leaving her a castle in Scotland. While roaming the castle late at night, she witnesses a Winter Solstice ritual designed to raise evil power, one Lady Jaye may become an unwilling participant in.
- Duke's been injured. The traitor has been discovered, now the former Joe is working for Cobra. The Joes must capture their former comrade, but he knows their methods, and can anticipate their moves. The Joes are soon captured, but an unexpected turn will reveal what's really going on.
- Cobra uses Tomax and Xamot's company Extensive Enterprises to purchase the Red Rocket food chain and use its location as a network of secret missile launching bases. But, the JOE team catches on to the conspiracy.
- 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?
- 1985–198622mTV-Y7.4 (124)TV EpisodeZartan and Cobra seize the Delta Space Station and destroy G.I. Joe headquarters. Shipwreck and Snake Eyes are lost behind enemy lines while Cobra Commander reveals his plan to deprive the world of electricity.
- 1985–198621mTV-Y7.4 (90)TV EpisodeAlpine and Bazooka make an ally in Quick Kick. Meanwhile, Tomax and Xamot betray Cobra Commander and take control of Delta Space Station and the Pyramid of Darkness for themselves.
- 1985–198621mTV-Y7.4 (89)TV EpisodeAs the Cobra leadership fight among themselves, G.I. Joe work together to destroy the Pyramid of Darkness.
- An explosion at a COBRA lab creates a cluster of explosive crystals, a substance that COBRA wants very much, so Cobra Commander kidnaps a group of people that he knows will get the job done, much to the shock of the Joes.
- Cobra steals a dangerous bacteria and an experimental growth serum. When the two are accidentally combined, a powerful monster is created that must be stopped by G.I. Joe.
- A mysterious person calling himself the Viper is leaving cryptic messages on one of the Joes answering machines. When the Joes investigate the messages, they encounter Cobra. The Joes and Cobra want to find out who is this mysterious Viper and how he knows so much about Cobra.
- The fight between the Joes and COBRA to retrieve a COBRA anti-matter pod may pale in comparison to the threat both face in the sunken U.S.S. Flagg: a certifyingly mad cook who believes he's the last surviving member of COBRA.
- Serpentor collects ancient artifacts from his past lives in order to gain power.
- A COBRA spy has infiltrated the Joes Base, and stole a security code that allowed COBRA to steal a highly advanced laser guidance system. Could the spy be Quick Kick's girlfriend, Amber?
- After Bree Van Mark and her father are saved by Lifeline after a COBRA attack, she becomes infatuated with the medic, which is bad for Lifeline, but good for COBRA, who uses Bree's crush on Lifeline to launch a deadly attack on the Joes.
- In an effort to take control of the world's fuel supply, Cobra launches attacks on the world's oil reserves.
- 1985–198622mTV-Y7.3 (96)TV EpisodeG.I. Joe sends teams to different parts of the world in order to stop Cobra from planting their electronic cubes. Meanwhile, Shipwreck and Snake Eyes continue to lay low behind enemy lines.
- When Shipwreck tries to show "reporter" Hector Ramirez and his crew that the Joe / Cobra conflict is real, he soon provides all the proof he needs, when COBRA captures them during an operation to steal volatile gas from a weapons arsenal.
- After successfully infiltrating Joe headquarters using very unusual means, COBRA plans on ruining Christmas in Keystone City by attacking the city in Joe vehicles. Can G.I. Joe stop COBRA from spreading their kind of "Christmas Cheer"?
- Cobra's latest scheme is to form a band, Cold Slither. Their music is filled with subliminal messages, that draws whomever listens to their concert. Then they can hold them for ransom. Shipwreck and a few other Joes, listen and get taken as well.
- After he's discharged from the Joe team, Dial Tone gets a job on a communications project, which unknowingly places him in the middle of another power struggle between Cobra Commander and Serpentor.
- While General Hawk attends a NATO meeting in Europe, Cobra infiltrates the Department Of Defense's computers and creates pandemonium at G.I. Joe Headquarters by promoting several inexperienced Joes to the rank of Colonel.
- In a plan to attack the world's cities with lava, COBRA kidnaps Dr. Shakur and his technology to accomplish this. Can the Joes save the doctor from Cobra's jungle base and destroy the weapon before cities are turned into literal hot spots?
- Cobra finds a tablet with a perfume used by Cleopatra. The scent makes men fall for which ever female wears it. The Baroness uses the formula to woo a rich single bachelor. Flint tries to stop her, but he's affected by the perfume as well. It's up to Lady Jay to stop her, she'll get some help from an unexpected ally.
- The good news: Flint goes to Pleasant Cove on vacation to see his relatives on vacation. The bad news: Flint finds out that they, and the whole population of the town are Cobra's brainwashed slaves, and Flint may soon be joining them.
- The COBRA Television Network is on the air, everywhere, on every channel, and the Joes must go into orbit to bring down Cobra's broadcasting satellite before COBRA takes over the world through the world of Television.
- When some of the Joes' personal items go missing, including a game program that simulates battle tactics, Cross-Country goes on a mission to track down the thieves and discovers they are robots controlled by Cobra Commander.
- Doctor Mindbender creates a device that allows him to enter the Joes' dreams and change them into nightmares, which begins to wreak havoc on the team's morale and mental alertness when they're trying to fight off Cobra.
- Cobra is suspected of shooting down an experimental military jet and the Joes must prove that they are behind the attack.
- COBRA gains new allies: the animal kingdom, through "High Freq", an animal mind control device. In a race against time, the Joes must stop "High Freq" before Mutt loses the fight against Junkyard, his best friend who is now his worst enemy.
- 1985–198622mTV-Y7.1 (101)TV EpisodeG.I. Joe sets up temporary headquarters on the U.S.S. Flagg. On the Delta Space Station, Dusty, Buzzer and Mutt work to warn the Joe team about Cobra's plan to plant cubes at strategic locations in order to create the pyramid of darkness.
- In an attempt to stop a world financial summit, COBRA decides to use an artificially created earthquake to get the job done. Can the Joes put a stop to COBRA before COBRA puts a stop to the meeting?
- Dr. Mindbender implants a device on a group of Joes, which allows him to affect their emotions using musical tones. Meanwhile, Lifeline tries to reconcile with his father, who hates his son's decision to be a Joe with a passion.
- When Cobra steals the gold from Fort Knox and puts it on a bullet train, G.I. Joe must find a way to stop the train.
- When the Aurora Borealis begins to go haywire and starts to melt the polar icecap, the Joes and a group of scientists go up north to try to prevent a disaster that could have global implications.
- COBRA invents a machine that can destroy paper money at a distance, and the Joes must get to the bottom of things and destroy the machine before COBRA can flood the world with their own dubious currency.
- While the fleeing from the Joes, Storm Shadow finds Arthur's legendary sword, Excalibur. In addition to stopping Cobra's latest scheme, the Joes must also return Excalibur to its resting place.
- When Lady Jaye decides to help a man get revenge against COBRA for injuring his family, they end up trapped on an island that is being used for the testing of a COBRA weapon that eliminates the power in vehicles.
- Flint and Lady Jaye are racing against time to get information to the Joes about COBRA's latest weapon, a vortex weapon that can create tsunamis and tidal waves, so the Joes can destroy the weapon before COBRA uses it to wipe out the U.S..
- When Slip-Stream is shot down by a female Strato-Viper near an abandoned Cobra laboratory, each tries to hunt the other down...until they discover that someone else is trying to destroy them both!
- The Baroness has found the Conch of the Sirens, used by the Sirens to control men, and has used it on the G.I. Joe and COBRA males. Can Scarlet, Lady Jaye, and Cover Girl find a way to break the Baroness's control over the men of G.I. Joe?
- COBRA has found the temple of Osiris and seeks the treasure within, and the Joes are in hot pursuit. But who will win at the end of the day: The Joes, COBRA, or something else?
- Cobra develops a powerful sound weapon and begins testing it in the Middle East. With the help of a Prince, G.I. Joe tries to stop them.
- 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.
- When on an island to repair a Joe vehicle, Bazooka sees a sea serpent, part of Cobra's plan to control the sea lanes, but when the serpent's remote is accidentally destroyed, it soon becomes an out of control, and very ravenous machine.
- Dusty and Footloose both vie for the attention of a female scientist during their mission: Getting her to the Joes so she can reveal the secrets of Cobra's powerful plasma cannon before COBRA catches them.
- Dinosaur bones, a cloning device, and a rapid growth formula all add up to Cobra's new addition to their ranks: living, breathing dinosaurs, a force that even the Joes may not be able to stop.
- After COBRA persuades Adm. Latimer, using his devotion to the Montana, to change sides and join COBRA. After COBRA installs a pulse weapon and the Montana becomes dangerous, Hawk makes a hard decision: Stop Latimer and sink the Montana!
- After a meeting with a friend who collects tissue samples ends badly, Iceberg goes to her base to find out why, and finds out that she and her uncle are being forced by COBRA to create animal-human hybrids, and he is the next test subject.
- Dial Tone, Leatherneck, Wet Suit and their date's night out at the 'Open Air' nightclub is out of this world, literally, as Serpentor sends the club into outer space, as part of a plan to obtain a valuable engine that runs on nitrogen.
- When approached by COBRA to perfect a anti-matter weapon, in exchange to walk again, Dr. Jeremy Penser agrees to the deal, but may regret it when his kid brother gets caught up in the fight between COBRA and G.I. Joe over the weapon.
- Leatherneck goes to CEC Academy to be it's guest of honor and soon finds out that it's a COBRA trap set up by his former cadet who's now a COBRA soldier, who plans to attack Parris Island to kidnap a major, all in the name of revenge.
- Bored with old games, the Gamesmaster decides to pit Cobra versus G.I. Joe in a high stakes game of life or death.
- When the Joes and COBRA find out that the nitrogen fuel that was stolen from the Joes can also "fuel" the growth of fruits and vegetables, they begin to do battle for the fuel, in a landscape of plants of gigantic proportions.
- In the jungles of Thailand, Dr. Mindbender is concocting a special chewing gum which will put whoever eats it at the mercy of Cobra.
- The Joes, along with British super secret agent Matthew Burke, must deliver to a weapons depository, a black box that, unknown to the Joes, contains a powerful nerve gas, a weapon that COBRA will spare no expense to possess.
- When the U.S. bought Alaska from Russia, they were supposed to get the Seal of Alaska. But the ship carrying the seal was lost at sea. Cobra has found the seal, terms of the agreement specified that the possessor of the seal owned Alaska. The Joes must get the seal from Cobra, but they're not the only interested party who's after the seal.
- Cobra tries to steal a spy satellite but Breaker stops them by forcing the satellite to crash in the African jungle. Efforts to recover the satellite by both Cobra and G.I. Joe are complicated by a tribe of African primitives.
- Desperately desiring eternal youth, Madame Vail makes Cobra an offer to get her longevity secrets for a price. In exchange, Cobra must provide Madam Vail with an abundance of young women with which she can keep her operation going.
- During a battle over the Suez Canal, a stray laser blast strikes a mysterious golden coil that transports G.I. Joe and Cobra back in time to ancient Greece. The Joes must find a way to return to the present...without changing history!
- Over spending by Tomax and Xamot leads to the creation of the Cobrathon, to raise five billion dollars, with the end of the world's law enforcement computers as a bonus. Can the Joes stop the Cobrathon before the world's law computers are?
- Due to a mix-up. Sgt. Slaughter takes Wetsuit's place in a martial arts tournament put on by an international criminal, but it is actually a contest to see who is good enough to serve COBRA in the capacity of an assassin.
- The Joes get a new weapon to fight COBRA: "WATCHDOG", a computer designed to keep track on Cobra's actions and assign Joes to go stop the threat. But Shipwreck soon finds out what this WATCHDOG is actually programmed to put it's "bite" on.
- Cobra amplifies the powers of a number of captured psionics one of whom is Airborne's kidnapped brother.
- When G.I. Joe visits a spa to investigate Cobra's theft of a special youth treatment, the team members suddenly find themselves at a disadvantage when they are transformed into little kids and old men!
- While battling COBRA, the Joes gets two visitors: The Oktober Guard (the Russian version of G.I. Joe), and aliens. Now the Joes and The Oktober Guard must join forces to find out who the aliens are, and what their purpose here on Earth is.
- Cobra takes over a dude ranch in an effort to control a nearby power station. G.I. Joe heads to the ranch to stop them.