A team of Joe soldiers are sent to investigate Cobra Pharmaceuticals. Their job is to infiltrate the facility to gather information on it's real purpose.
With the help of an inside source, the Joes infiltrate a Cobra stronghold where Mindbender and McCullen work together to produce the ultimate exo-armor weapon.
The Joes locate a bio-viper manufacturing facility and are met with resistance from Firefly, a Cobra saboteur who threatens to burn the surrounding town to the ground.
On a mission to capture Mindbender, the Joes become entranced and are trapped in a cult-like commune run by the eerily charismatic twin brothers Tomax and Xamot.
The Joes enlist the help of sea captain Shipwreck to help them transport a canister of evidence abducted from a Cobra lab; unfortunately the trip is anything but smooth sailing.
Investigating Cobra's 'BioDag' delivery system, the Joes travel to Scotland where they become trapped inside Destro's castle! A game of cat and mouse ensues as the Joes search for an escape from the deadly mansion.
The Joes infiltrate a global telecommunications conference hosted by the Baroness at her ancestral castle. There, they uncover a Cobra plot to enslave the world via cell phones, while meeting an unexpected ally.
The Joes raid a Cobra medical facility looking for information on the alleged inhumane experimentations being conducted as well as a mysterious 'Patient X'.
Investigating a missing kid from Tunnel Rat's old neighborhood, the Joes head to Brooklyn, where they discover an urban legend about a monster in the sewers may in fact be true.
Heavy Duty is recruited by Flint to help bring in his cousin Roadblock; unfortunately for both men and the Joes, Major Bludd is seeking vengeance for the scars received in their last encounter.
Investigating a series of mysterious earthquakes, the Joes head underground and discover an elaborate network of tunnels being constructed by Cobra to connect their multiple strongholds across the country.
Cobra works to finalize deployment of a scientific apparatus that could give them unimaginable power; and it turns out Scarlett holds the key to its use.