Fed up with Cobra Commander's leadership, Dr Mind Bender comes up with an idea to create the ultimate leader using the genetic material from some of histories greatest conquerors. Needless to say Cobra Commander isn't too supportive of the plan.
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.
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?
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..
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!
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!
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.
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.
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?
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.
Cobra sits in a room watching a simulation of a woman going through a beauty transfer. The first woman is old and decrepit and the other woman is young and beautiful. The young woman begs to be let out of the machine but to no avail as her face is left with no eyes or mouth. Then Madame Vail makes Cobra an offer to get her longevity secrets for a price. Cobra must provide Madam Vail with an abundance of young women with which she can keep her operation going. Dr Mindbender calls it "Operation: High Fashion." Meanwhile Low-Light and Dial-Tone are helping Low-Light's ...
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.
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.
The investigation into the theft of a youth formula leads Flint, Lady Jaye, and four other Joes to the COBRA owned Ageless Care spa, where they find they might have some trouble stopping COBRA after being turned into young kids and old men.
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.
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.
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 battleground to fight COBRA: ancient Greece, when a stray laser blast hits a mysterious golden coil, sending the Joes and COBRA back in time, where the Joes must find a way to return to our time, without changing history.
Cobra hacks into the the Defense Department, and promotes Life Line, Dial Tone, and Shipwreck to full Colonels. With General Hawk away at a conference, these three are now in charge, which causes major issues when Cobra launches an assault.
Dr. Mindbender creates the Somnia machine, a device which he plans to cause disarray in a number of Joes by entering their dreams and change them into nightmares, hoping to affect their morale and mental stability during their waking hours.
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.
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.
Joe communications expert Dial-Tone's re-enlistment to the G.I. Joe team is "turned down" effectively terminating his position. After being down on his luck and unemployed he ends up being tricked into helping the Cobra Commander raise a monster from the ruins of Destro's family castle in order to destroy Serpentor and for the Commander to re-assume power.