The story of follows a rare timeline where Cobra actually achieves its ultimate goal of world domination. Told through an 80s-style comic book aesthetic, the narrative splits the experience between Joe and Cobra perspectives across 17 missions. The Fall of G.I. Joe: "C-Day"

The Joes eventually manage to shut down the device and restore order, but the peace is short-lived.

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

: The story ends on a classic cliffhanger; as the Joes celebrate their hard-won victory, Roadblock and Mainframe receive an alert of a brand-new Cobra threat, ensuring the conflict remains eternal.

: 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.