The story turns to two young women named Margaret and Madlax, who apparently have little in common and do not know of the other's existence at the beginning. Madlax is a legendary mercenary and assassin in the fictional civil war-torn country of Gazth-Sonika, who cannot remember her past or indeed her real name before twelve years ago, when the war started. The other main character is Margaret Burton, the sole heir of a wealthy aristocratic family in the peaceful European country Nafrece. Twelve years before the story begins, an airliner Margaret and her mother were on crashed over Gazth-Sonika, and its passengers, as well as Margaret's father who led the rescuers, have been missing ever since. Margaret, however, mysteriously traveled back to Nafrece on her own, losing her memories prior to her return; the only thing she recalls is a single word, "Madlax". With this thread linking the two girls, they both independently start investigating the powerful crime syndicate Enfant after its enigmatic mastermind shows interest in both of them.