Two years have passed since the end of Metal Slug, when Capt. Marco Rossi and Lt. Tarma Roving of Peregrine Falcon Strike Force defeated and apparently killed the evil General Morden, who had staged a coup d'état against the worlds' governments. Since then, various factions sympathetic to Morden have been in operation, but have always been considered insignificant. Recently, however, they have begun to act in unison, and army intelligence concludes that the only way this could happen is if Morden himself is in fact still alive and is attempting a new coup. As such, Rossi (now a Major) and Roving (now a Captain) are sent to once again battle Morden. However, such is the importance of the mission, that they are accompanied by two members of the Intelligence Agency's Special Ops Squad S.P.A.R.R.O.W.S.; Sgt. Eri Kasamoto and Sgt. 1st Class Fiolina Germi.
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