When their investigation into the disappearance of an operative leads them directly to The Five Republics, the Social Welfare Agency sends mechanically-enhanced cyborg Triela to infiltrate the organization. However, she meets her match in the form of Pinocchio, one of Padania's assassins whose skills with a knife are exceptional. Meanwhile, after a long period of hospitalization, Angelica has recovered enough physically to return to the field. But due to the side effects of her conditioning and her addiction to the medicine prescribed to her, is she mentally ready?
A young man awakens in an abandoned warehouse with no memory of his past. As he leaves the room and ventures further into the warehouse he is attacked by a girl in a mask; she tells him that in order to live he must come at her with all his might. After a fight for his life, he manages to overpower the girl, learning that he is to be trained as a Phantom - an assassin for the Inferno organization. He is also given a new name: Zwei. For three months, Zwei is trained by the girl in the arts of assassination until he has just one final test: to kill a living human being.
Both shows have the main character being a girl who is an assassin and a guy character who assists them. The girls are controled by other in both shows. In gun slinger girl the girls work for the government while in Phantom they work for a criminal organization.