A teenage Japanese boy wakes up to find himself alone in an empty room with no memory of his own identity or past. He surveys the room he is in and discovers he is a Japanese tourist and suddenly realizes the only thing he can remember is that someone was trying to kill him. While he explores the seemingly abandoned building, he is suddenly attacked again by the masked person from his memories and is told to fight with everything he has or die. Meanwhile, someone is remotely watching his actions. Deciding that he wants to live, he fights back and momentarily gains an advantage; as he attempts to make a killing blow, the mask cracks and his attacker is revealed to be a girl. Instead, he attempts to leave but finds himself surrounded by a desert and the girl, no longer attacking him and introduced as Ein, tells him he will now either live on as an assassin named Zwei or be killed. These scenes are interspersed with a flash forward of Zwei and Ein working together as "Phantom" on an assassination mission. Ein, poses as a maid, along with Zwei, manage to eliminate an entire household of armed guards and the head of a mafia boss in Las Vegas, once again proving their absolute power and indispensability to a mysterious organization called Inferno.

Ein conducts personal training to Zwei after agreeing to work with Inferno for several days, ranging from sparring in martial arts to small arms use in order to hone his skills as a potential Inferno assassin in upcoming Inferno-approved missions. Claudia enters the complex right after Scythe Master picks up Ein without revealing her presence and tells Zwei about the objectives of Inferno, as well as to give "hope" to Zwei that he can find out who he is before she leaves him with a goodbye. Meanwhile, the Scythe Master deploys Ein in an assassination mission somewhere in the United States to kill a person of interest.

Ein is dispatched to take out Inferno henchmen in a warehouse district as part of a plan hatched by Raymond and Claudia to eliminate Scythe Master. Claudia, in summoning Zwei to her mansion, gives him his Japanese passport and reveals his real name to be Reiji Azuma. When Zwei is in shock, Claudia offers him a place alongside her after revealing her feelings. However, Reiji returns back to the complex hideout to see Ein wounded after being shot by Lizzie when the two confronted each other. Reiji receives a call from Claudia, telling him that he would be killed if he would assist Ein in any way. Refusing to be intimidated, Reiji helps Ein remove the bullet from her wound before he secretly evacuates her from the complex in order to avoid being tracked down by Inferno for refusing to join with Claudia in her plans to take over Inferno and get rid of Scythe Master.

Three months after Reiji's near fatal death at the hands of the Scythe Master in the wharf district of San Francisco, Inferno was able to take control of some of the crime families in the eastern area of the United States and integrate them under Inferno control under Claudia's command. Isaac confides to Raymond that Claudia may be acting suspicious after the conference. Claudia was later seen to be visiting the grave of Romero McCunnen. Reiji, now taking the codename of Zwei again after recovering from his wounds, is declared to be Phantom by Raymond after killing off multiple gunmen at an unknown warehouse complex.