The game's story centers around a group of knights called Chevalet Blanc and how the protagonist and her knights take back the kingdom of Elesius, which is being controlled by the Council of Elder Statesmen. The Princess Royal of the kingdom died in an accident, and the king is too ill to rule, which brought about the rise of the council. Like other Wild Arms titles, this takes place on the dying planet Filgaia, this time where the remaining natural resources, food, land and financial assets are at the center of continued armed confrontations. Despite this, Elesius is one of the few peaceful places on Filgaia.

Chevalet Blanc's beginnings are anything but noble: two Drifters, Clarissa Arwin and her adoptive brother Felius come to the kingdom of Elesius in pursuit of a Drifter named Rupert Dandridge, who five years ago slew Clarissa's mother, itinerant archaeologist Melissa Arwin, and took from her the powerful sword "Iskender Bey". Clarissa's mission is solely to retrieve that sword, but before much time has passed, she has been confused for Alexia Lynn Elesius, the heir-presumptive to the throne of Elesius who died a year ago under mysterious circumstances. While the council's rule is generally self-centered, their most constant presence in Elesius takes the form of the "Martial Guard", a mercenary "peacekeeping" force who steal and oppress with impunity. To rally the citizens of Elesius, Clarissa publicly declares herself to be Alexia, and founds a rebel movement called "Chevalet Blanc", after the Founding Knights of Elesius. Its established goal is to defend the citizens of the nation, which will involve defeating the council. The fact that Rupert is the leader of the Martial Guard only strengthens Clarissa's resolve.