One year has passed since the end of the original A Real American Hero series, but a new threat looms on the horizon. The President has reactivated the G.I. JOE team headed by General Joe Colton and headquartered in a new complex called The Rock.

The G.I. JOE team is sent on a rescue mission for Scarlett and all return except for Snake Eyes. Is he dead or alive? The hunt is on to find out. Meanwhile, Duke is captured in the Amazon forest and "interrogated" by a Crimson Guardsman, all leading to a massive Ninja showdown.

COBRA COMMANDER has been absent for a year, his whereabouts unknown, but while officials in the government take that as good news the G.I. JOE team knows better. Meanwhile, The Phoenix Guard is being proposed to replace the team led by former G.I. JOE commander Philip Rey.

A former teammate turned enemy seeks the answers for a past that is hidden from even himself, and the Baroness, one of the Cobra's most deadly members, is at large and visiting violent retribution on all her enemies. Collects issues #19–24 of G.I. JOE: America's Elite.

The struggle between G.I. JOE and COBRA has been waged for years and through diligent service and sacrifice, the G.I. JOE team has managed to keep COBRA from achieving its goal, until now. World War Three begins. Collects issues #25–30 of G.I. JOE: America's Elite.

The conclusion to the World War III storyline is collected in the last volume of America's Elite, Disavowed. Collects issues #31–36.