Chicago is hit with some kind of terrorist weapon. The President reactivates the Joe team. And General Joe Colton is put in charge. The Joe team has a new headquarters called The Rock in Wyoming. Roadblock, Scarlett, and Shipwreck go to Chicago to investigate where they discover that the object that hit Chicago was something from the US government. Stalker, Snake-Eyes and Flint attack a Cobra cell in Germany. Storm Shadow meets Gen. Joe Colton. Vance Wingfield is the architect of the Chicago attack.
One year after the events in One year after the events in G.I. Joe 43 .
Subject: Intel Briefing
From: Central Data Desk
To: Internal Command
"Effective immediately: The President has re-activated America's Elite counter-terrorist unit - code name G.I. Joe. Core Roster to be comprised of agents/code names: Duke, Flint, Roadblock, Scarlett, Shipwreck, Snake-Eyes, Stalker and Storm Shadow. Specialists activated as needed. Unit Status: strictly covert at all times. All Operations classified top secret Primary ongoing mission: track and eliminate all Cobra cells globally. Secondary ongoing mission: Elimination of extremist groups as they arise."