When the Joes seek to recover a sample of anti-matter from a sunken ship, Zarana is sent to their headquarters to sabotage the operation. She and Mainframe discover they have feelings for each other. In the aftermath of a battle, the USS Flagg is sunk.

A surprise attack by Cobra, using the new BATs, reveals that the Joes have gotten sloppy. General Hawk asks Sergeant Slaughter to help whip the team back into shape. Meanwhile, a series of dreams prompt Dr. Mindbender to concoct a plan to build a new Cobra leader from the DNA of long-dead conquerors. A package downed Night Raven reveals that Zartan has been asked to expand his team of Dreadnoks so he turns to his siblings, Zandar and Zarana for help, and the Joes investigate and discover the plan, only to be cornered by Thrasher and his Thunder Machine.

An aging admiral learns that his ship is to be scrapped, and he turns to Cobra for help. Cobra renders his ship impervious to electronic vessels, so G.I. Joe must use the two-hundred-year-old USS Constitution to defeat him.

Leatherneck attends graduation ceremonies at a new academy and discovers it run by former enemy Buck McCann, who is loyal to Cobra. Leatherneck must foil McCann's plan to destroy Parris Island Marine Academy.

Cobra takes DNA from the tombs of Ivan the Terrible and Alexander the Great. Sergeant Slaughter retrieves a DNA pack from Cobra's raid on Sun Tzu's tomb, and from it the Joes surmise that Cobra is building a new breed of soldiers. Dr. Mindbender intends to use Slaughter's DNA as a replacement, and so feigns defeat as a ploy to retrieve the sarcophagus of Genghis Khan and capture Slaughter.

Cobra discovers an Asian tree sap that brainwashes people, and uses it to enslave the native population. Leatherneck must care for four orphans while the other Joes try to prevent Cobra from marketing the sap as chewing gum.

Bree Van Mark, a cute wealthy woman, develops a crush on Lifeline after he rescues her and her father from a sinking yacht during a battle between G.I. Joe and Cobra. Lifeline discovers that Cobra is after Bree's father, a wealthy industrialist whose holding include a defense company. But the Joes think that Bree is working for Cobra since some of her gifts, including a gold plated helicopter, have backfires. She flies off in a Tomahawk taking Lifeline with her. They head to a cabin in the Rockies and are followed by Cobra. Lifeline, who is a pacifist, must fend off Cobra until the rest of the Joes arrives.

Cobra Commander sabotages Dr. Mindbender's first experiment, and it rises as a hideous monster. Sergeant Slaughter briefly escapes, then is recaptured but manages to destroy his DNA sample. The second attempt is successful, and Serpentor is created. Meanwhile, a Joe search party is sent to Cobra Island to rescue Slaughter and learn more about Cobra's plans.

International superspy Matthew Burke volunteers his services in helping the Joes transport nerve gas to a safe facility.

Lady Jaye disguises herself as the Baroness in order to learn about a Cobra weapon created to form whirlpools and tidal waves.

Cobra stages a telethon to raise money for a computer virus that will bring down all the computer systems in the world, as the Joes try to rescue Sci Fi and Lifeline...

The Joes visit an arctic region where Icebergs Girlfriend is collecting samples of animals tissue for her Uncles research at the Tropadome. Icebergs goes to the Trapadome only to be captured by Doctor Mindbenders new mutant animal army...

When an orphanage is accidentally damaged during a battle, Shipwreck and other members from G.I. Joe volunteer to help repair it. While doing so, Shipwreck is dragged into telling the children a fairy tale...a typically cockeyed Shipwreck extravaganza!

Madame Vail (voice- Mary McDonald Lewis) agrees to sell her youth transference machine, which makes people young (and beautiful), in return for kidnapping some of the world's top models, who's youth and beauty will be transferred to the machine's user. One of these models is Low Light's sister, Una...

The Joes stumble upon an oil platform being used by Cobra to try to salvage the anti-matter pod that went down with the USS Flagg and the Cobra helicarrier. The Joes investigate, followed by Zartan and the Dreadknocks, but both teams are captured by an insane Cobra cook named LaCar...

The Joes send teams out to guard the tombs on Zartan's list, but each team is defeated in turn: by Zarana in Egypt, the Crimson Twins in Paris, the Dreadnoks in the Yucatan, and the Baroness in Transylvania. Duke's team and the Oktober Guard are in a standoff with BATs while defending the tomb of Ivan the Terrible.

Sergeant Slaughter accompanies Sci-Fi to a science fiction convention, where Dr. Mindbender recruits a handicapped scientist to repair his latest weapon. Mindbender's false promises to enable the scientist to walk again lead him to walk all over his brother.

Seargent Slaughter and the rescue team escape Cobra Island, but Serpentor captures Washington D.C. just as the Joes learn about the new leader. But Serpentor's lack of experience in modern warfare puts Cobra at a disadvantage when G.I. Joe stages a counterattack.

Cobra steals Madame Versalles youth treatment. The Joes try to figure out why and that leads them to the Ageless Care Spa, where lady Jaye, Mainframe and Dial Tone are turned into seven year olds...

Wet-Suit and Leatherneck have never, ever got along but their heated rivalry must take a backseat when Serpentor begins collecting artifacts from his former lives to gain power, and Leatherneck is poisoned trying to stop him. Wet-Suit has to prove he doesn't have any hard feelings for Leatherneck, as he and Lifeline risk their lives trying to recover an antidote from Serpentor's blood.

Cobra seizes control of a new satellite for use with a new transportation device, and Duke is captured in the attempt. The G.I. Joe team learns that they must build their own device to defeat Cobra.

The Joes travel to the arctic to retrieve rare minerals to fuel their MASS device, but Cobra ambushes them, and Snake Eyes is presumed dead. Duke manages to escape the Cobra base with the help of a slave girl, but he is injured and cannot remember the base's location.

Snake Eyes returns home with the help of a wolf and a blind man. The Joes and Cobras battling for undersea elements must join forces to escape giant tubeworms on the ocean floor.

G.I. Joe tries to throw off Cobra with a false surrender while mounting a mission to the Ring of Fire for the third element. Destro sabotages the operation but is pursued by Scarlett.

Destro returns to Cobra base and seizes control of the operation from the Commander. The now-captured Scarlett and the slave girl organize a slave revolt. Duke's memories under sensory deprivation lead the Joes to the Cobra base where a final battle takes place. Cobra Commander is captured and taken to prison, but Destro escapes. The battle is over but not the war!