Cobra Commander uses his control of M.A.R.S. weapons to create conflict all over the globe, in a last bid to gain control of the world. G.I. Joe counters by going on the offensive, mobilizing the entire G.I. Joe roster, and launching missions to capture Cobra agents still at large. Meanwhile, Cobra Commander recruits soldier Nick Bailey, making him the last member of a new elite Cobra unit code-named "The Plague". The main G.I. Joe team heads to Israel, where they help stop an assassination attempt. While the team is away, Cobra Commander attacks Washington, D.C., taking over the White House and capturing the President. Cobra also takes over Fort Meade, while Alexander McCullen attacks London and France with the Iron Grenadiers.