: Victory doesn't bring peace to Cobra. Within the "Cobra household," prominent members like Destro and the Baroness begin working on their own shadow plans, undermining the Commander’s leadership while attempting to solidfy their own power.

: With the world's militaries paralyzed, Cobra forces defeat the G.I. Joe strike team globally. Many Joes, including leader Duke , are captured, leaving the remaining team fractured and on the run. Internal Strife and the Resistance

: Scattered survivors like Scarlett, Roadblock, and Snake Eyes must regroup and find "The Mold," a critical relic needed to neutralize the Blackout Sphere. They eventually fight to recapture the USS Flagg and infiltrate Cobra’s headquarters. Ending and Legacy

: Cobra Commander uses intelligence stolen from NASA to launch a surprise attack on the USS Flagg . By seizing control of the G.I. Joe satellite network, Cobra generates a "Blackout Sphere"—a global EMP that disables all electrical equipment worldwide except for Cobra's own assets.

: The game culminates in a dual-boss battle against Destro and the Baroness in the final level.

The campaign begins with a massive, coordinated Cobra strike known as .

See the initial Cobra attack on the USS Flagg and the activation of the Blackout Sphere: