The rebellion orchestrated by General Morden to bring about a new global regime is now ancient history, and order and peace has begun to return to the world. Morden, brought back into power, was attempting another coup d'état, but government forces got wind of the plot beforehand and pre-empted the impending assault.
Instrumental in squashing Morden's rebel forces, Marco and Tarma of the Peregrine Falcon Strike Force are ordered to lead the team after their earlier requests for resignation were denied. Although General Morden has been written off as "missing" by his followers, they have hidden themselves throughout the world, and Marco and Tarma's abilities and experience are seen as a necessity to destroy remaining rebel strongholds, one by one. Throughout the furious fighting against the holdouts, Marco and Tarma cannot help but suspect Morden's involvement in this new evil plan for world domination.