Two years have passed since the end of Metal Slug, when Captain Marco Rossi and Lieutenant Tarma Roving of the Peregrine Falcon Strike Force defeated and killed the evil General Morden, who had staged a coup d'état against world governments. Several factions sympathetic to Morden were in operation, but are considered insignificant. They begin to act in unison, and army intelligence concludes that the only way this can happen is if Morden is still alive and attempting a new coup. Rossi (now Major) and Roving (now Captain) are sent to once again fight Morden. They are accompanied by two members of the Intelligence Agency's SPARROWS Special Operations Squad; Sergeant Eri Kasamoto and Sgt. 1st Class Fiolina Germi.