The plot of Front Mission 2089 revolves around a group of mercenaries led by Ernest J. Salinger. Given the codename "Storm", Ernest conducts sorties near Mail River. While many of the sorties involve basic reconnaissance and data collection, the mercenaries detect abnormalities by the border. Mercenaries hired by both sides begin mysteriously disappearing, and many of them were last sighted near Mail River. Unsure whether or not the mercenaries are deserting their duties or are truly disappearing, Storm's superior officer Falcon orders them to investigate these disappearances. During their investigations, Ernest and his group come across an unknown mercenary outfit known as the Vampires.