Episode list

Shipwreck 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.

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.

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...

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.

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.

Dissatisfied with Cobra Commander's leadership, Dr. Mind Bender proposes genetically creating an ideal new leader.

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.

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.

Cobra tries to undermine a global anti-terrorism conference by sending Zartan to replace an ambassador.