One year after the event of Metal Slug 7. A special disc that contains deep and intricate secrets about the Metal Slug project is stolen by a mysterious group called the Ptolemaic Army, whose speciality lies from within archaeological excavation and espionage. Marco and Tarma of the Peregrine Falcon Strike Force follow in hot pursuit against the group and in the process are joined by Eri and Fio of SPARROWS. Together once more, the quartet investigate the shrouded objective of the Ptolemaic Army, who over time grows more powerful as they are joined by a mysterious masked man and his followers.