The story opens up with Madlax, a very deadly and sexy female gun-for-hire parachuting from a helicopter deep into a Latin American jungle, where she is to recover a floppy disk from a unskilled teenage rebel fighter name Peter Anyan. Later when the enemy army closes in on Peter, Madlax puts on a long flowing evening gown, and using her supreme, almost supernatural agility, and shooting skills, ambushes the army to try and save him.
Madlax gets and an assignment from her boss, "Three Speed", to kill Guen McNichol, the Commander-in-Chief of the Gazth-Sonikan Royal Army. Madlax is amazed when she finds out McNichol is the one ordering his own assassination. Full of female curiosity, Madlax goes to hotel where the commander is staying, overpowers the maid, and sneaks into his room, to meet, talk with him, and find out more, the night before is scheduled to kill him.
In Nafrece, Margaret meets Carrossea Doon, who may know something about her Book. In Gazth-Sonika, Vanessa is desperate to find the encryption key to unlock the data, but a sudden call from SSS disrupts her plans
All pieces are in motion: Limelda desperately tries to cope with the truth about her whole life, Madlax searches for the truth behind her past, Margaret is ready to deal with Enfant if they help her to find Vanessa, and Vanessa herself hurriedly learns to shoot.
Fighting their way through all cordons and front lines, Madlax and Margaret strive to meet the only person who can share with them the knowledge about Margaret's Holy Book and their own destinies. Meanwhile, Carrossea makes an unexpected move, too.