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.
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?
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.
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.
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.
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.
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!
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.
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!
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.
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.
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.
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.
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!
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.
