Episode 1
Recruited soldiers escort Army intelligence to investigate Cobra's facilities and are surprised by what they find.
Episode 2
The Joes track a Cobra Bio-Viper while fleeing the military to evade punishment for a crime they did not commit.
Episode 3
The Joes stop the Baroness' mercenary from completing his planned assassination.
Episode 4
The Joes train with Snake Eyes at his dojo and learn about his connection to Storm Shadow.
Episode 5
The Joe team regroup after an ambush from Storm Shadow and must come up with a plan to rescue Jinx, who has been kidnapped.
Episode 6
Duke protects his family, who have been targeted by Cobra, while the team sneaks into Cobra's Christmas party.
Episode 7
Baroness tries to hijack the Joes as they're being transported by Flint and Lady Jaye, so she can gain control of the secrets stored on Cobra's drive.
Episode 8
Scrap-Iron kidnaps Tunnel Rat and uses him to test a weaponized exo-suit. Roadblock attempts a rescue by allowing himself to be kidnapped as well.
Episode 9
The Joes go on a mission to stop Zartan and his motorcycle gang from terrorizing a small town.
Episode 10
Duke is arrested while buying parts for the Coyote, and the Joes have to break him out of jail before others can find him.
Episode 11
The Joes penetrate a Cobra facility where an exo-armor weapon is being developed.
Episode 12
The Joes try to destroy a bio-viper facility, but are hindered by Firefly, a saboteur for Cobra.
Episode 13
Tomax and Xamot entrance the Joes and hold them in a commune.
Episode 14
Lady Jaye and Flint use Zartan to track the Joes. Meanwhile, the Baroness tries to sneak a camouflage suit to Cobra
Episode 15
The prototype Shadow-Vipers and Storm Shadow follow the Joes to Canada, where they are hiding out with Snow Job.
Episode 16
A sea captain helps the Joes transport a bio-viper canister taken from Cobra's lab, but things go wrong on the journey.
Episode 17
In Scotland, the Joes become trapped in Destro's castle while on a mission investigating a Cobra weapon.
Episode 18
The Joes uncover a mind-control scheme at the Baroness's château.
Episode 19
The Joes uncover a deadly Anaconda Strain virus while searching for a missing scientist and learn of Cobra's plan to profit from the sale of its antidote.
Episode 20
Cobra's medical facility is raided by the Joes, who are searching for Patient X.
Episode 21
The Joes head to New York to find a missing kid. While investigating, they encounter a Sewer Viper being pursued by a Mindbender.
Episode 22
A Cobra commander is attacked by a ninja and forced to escape to his secure facility. Meanwhile, Snake Eyes and Scarlett sneak into the commander's facility.
Episode 23
Flint gets help from Heavy Duty to capture Roadblock. Meanwhile, Major Budd seeks revenge against the Joes.
Episode 24
A series of earthquakes alerts the Joes to a network of tunnels Cobra is constructing to link its strongholds around the country.
Episode 25
Cobra plans to increase its power by deploying the MASS device, but Scarlett plays a key role in its operation.
Episode 26
The Joes attack Cobra to stop the use of a dangerous device, expose its owners and clear the team's name.
