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.

After more training with Ein, Zwei is going to be tested. He has to kill a man named Captain Wallace of the Navy SEALs, who sold weapons to Inferno, but because they weren't his only costumers and he sold many weapons to terrorists. Wallace eventually sullied the name of Inferno and put them in danger of being suspected by the FBI after an FBI agent was found dead in Mexico, forcing him to beat Zwei and defeat him in a duel to the death in order to allow Inferno in rebuilding his life all over again. After hesitation of killing Wallace and almost being killed by him, his assassination skills awake and he shoots Wallace in his head after wounding him by using a combat knife to stab him in Wallace's right arm.

Ein and Zwei are given the order to kill Don Lucio, the boss of a mafia family based in Dallas, Texas as their first assignment together. Because he never leaves his mansion, the two Phantom assassins have one chance in either making the mission work or not. With the unexpected help of Scythe Master, who drove in to assist the two assassins in making their getaway, Ein and Zwei were able to successfully kill their assigned target and flee for safety. The two were later sent abroad to lie low due to the success of their mission. Zwei contemplates on how he had been indoctrinated successfully by Inferno as a now skilled hired assassin and killer.

Inferno tries to establish contact with a mafia family somewhere in Los Angeles led by Tony Stone, who was currently busting up individuals selling drugs at Melanie Square personally. During this time, Claudia invites Zwei over to her estate in order to act as her secondary bodyguard and a spy to maintain recon on the mafia itself. When the meeting for Inferno to conduct its influence on Melanie Square was not working in their favor as Tony refuses to do so, Ein and Zwei are deployed to wipe out the entire mafia and assassinate the wife and only child of Tony to prove that Inferno is a force to be reckoned with.

The surviving members of Tony's mafia plan revenge against Inferno by planning to release crucial information on certain mobsters who are suspecting of supporting Inferno from behind the scenes to discredit them and be eliminated from the inside. However, Inferno plans to conduct an assassination spree on all anti-Inferno mafia personalities in the West Coast of the United States with Ein and Zwei being in the forefront working with Lizzie to carry out the assassinations on the orders of its top leaders under insistence from Claudia. Thanks to their efforts, Inferno was able to consolidate their influence in the area.

Ein leaves Zwei to meet Scythe Master, while Zwei decides to practice his driving while she is gone. However, McCunnen appears and begins to move in on Zwei, to which Scythe Master warns Ein not to let the infatuated McCunnen steal Zwei away. Meanwhile, Ms. McCunnen starts to form her own plans within Inferno. Later on in the day, Zwei has a dream about his past, where he witnesses a murder of an Inferno target, shot by Ein. After fleeing for days, Zwei is caught by Ein and Scythe Master, who seems interested in his innate ability to survive. After waking up, Zwei asks Ein whether she has had any dreams about her past, to which she say she has. However, she is apathetic and uninterested in finding out her past. Later on, the two are asked to back up a Phantom operation that consists of stealing 500 kilograms of cocaine. Right as they are about to head out, Zwei is asked to switch jobs and protect Ms. McCunnen in Lizzie's place instead. Though hesitant at first, Ein insists that Zwei follow Ms. McCunnen's orders, so Zwei agrees. Meanwhile, Raymond McGuire and Ms. McCunnen's plans to get rid of Scythe Master are revealed.

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.

Reiji, now rejecting his Phantom codename Zwei, escapes with Ein while the rest of Inferno gets worked up on their escape. Ein had planned to commit suicide by shooting herself as she had no place to call home before Reiji stops her from killing herself. He consoles her and gives her a new name and identity of her own: Elen. Elen encounters Scythe Master in an alley after gunning down an armed man looking for her. Lizzie and Claudia capture Reiji in a parking lot when he was about to hotwire a car. Reiji was subsequently interrogated, being accused of assisting Scythe Master in rebelling against Inferno. Claudia offers Reiji assistance in saving Elen, locked up in an unknown location, by releasing his restraints and offering him a pistol for him to use. In return, Reiji promises Claudia that he would take care of Scythe Master.

Lizzie and her group are dispatched by Claudia with the objective being to assassinate the Scythe Master, upon learning of his whereabouts. Although reluctantly, Lizzie also admits Reiji into the assassination team and are dispatched to the wharf in San Francisco. They were able to defeat Scythe Master's reinforcements with Reiji being able to corner him when Elen appears just in time after Reiji shoots his pistol at him. Reiji drops to his knees after seeing her take the bullet for Scythe Master, collapsing due to the new gunshot wound. Taking advantage of the change in his situation, Scythe Master finishes Reiji off by shooting at him multiple times before he collapses into the sea. He is later found to be alive, but wounded from gunshot wounds on his body.

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.

Six months later, Reiji has just taken down the No.2 man in the Gambino family in his latest assignment, leaving Inferno sole control of the East Coast and spreading fear to the criminal underworld. Claudia receives permission from McGuire to directly handle negotiations with the Godoh family in order to control the monopoly of exports to Japan. When she and Reiji go off to meet representatives of Godoh in Isaac's territory, they find that all the men, including some of Isaac's, are killed by a professional assassin. Reiji finds a passerby killed in the crossfire. When he returns later to the scene to mourn, he finds a girl named Cal Devens, who tells him that it was her sister Judy who was killed. She tells Reiji that she knows who killed Judy and insists on working with him to investigate. Reiji relents and takes Cal with him, as he feels an affinity with her since both their lives were destroyed by Inferno.

Reiji is accused by Isaac of lying to hide Cal away from him as he wanted to interrogate Cal regarding the shootings in his turf. Reiji and Lizzie face McGuire, Isaac and Claudia on whether the former was hiding something from them. He promises to train Cal to be an assassin like him as he claimed she has the potential to be a killer like him. Before going to the meeting, Cal showed him the $5 million dollars she hid from the scene after Judy was killed by stray fire and pleading to him to kill those responsible for Judy's death yesterday. In the end, Reiji is conflicted on how he could avenge Judy's death and train Cal to be a successful assassin at the same time.

Reiji and Cal go out to get clothes before he started to train her in firearms when he was told by Lizzie that McGuire wished to get details on Cal's training. Meanwhile, Claudia tells Reiji that she plans to use Godoh and his henchmen to smoke out Isaac as she believes that he's the one responsible for the shootings back in Los Angeles. Reiji shadows the Godoh group in Las Vegas before he finds one of the group's henchmen killed in his Las Vegas hotel room. Reiji pursues the supposed assassin towards the elevator when he caught a supposed glimpse of the assassin, who he thinks is Elen. However, Reiji thinks that Elen can't be alive since he remembers accidentally shooting her when the girl tried to protect Scythe Master from being killed back in San Francisco.

Godoh is furious over the murder of his men once again and demands an explanation with Claudia promising that she'll do everything in her power to smoke out the culprits responsible. Reiji was given the assignment to locate the culprits responsible for killing Godoh's subordinates. Accepting the assignment, Reiji brings Cal along to assess the situation and determine the potential sniping locations where the assassins will use to disrupt the meeting between Godoh and the executives of Inferno. During the meeting, Reiji was able to gun down one of the armed assassins during his counter-sniping assignment with Cal when he finds out that the sniper he killed is Randy Weber, the right-hand man of Wisemel. However, a second sniper rifle is heard when the meeting is interrupted. Godoh and his remaining subordinates point their sidearms at the Inferno executives. Reiji doesn't know that Ein had survived, being the second sniper for interrupting the Inferno-Godoh conference.

To appease Godoh, Claudia shoots and kills Isaac as the one responsible for the sniper attack. Later, Reiji confides to Lizzie that the sniping occurred after Randy Weber was killed, which means it wasn't part of Isaac's plan. Reiji plants the money that Cal stole at Wisemel's mansion to implicate him further in his treachery. Cal offers to help Reiji in his assassinations, he doesn't want her to get involved any further but Cal still wants to help Reiji, as she feels isolated as Reiji is alone in this assassin lifestyle. Cal wants to be Reiji, with him Forever. Though Reiji feels that with Cal here, Cal won't have to help him with his Phantom work as he will stop his current life so he can be with Cal. After confirming Isaac's treachery, McGuire makes Claudia his new second-in-command. Scythe Master frames Reiji for killing Godoh's man after he shows them an incriminating photo of him. Reiji receives a call from Lizzie, telling him to help her deal with some restless remnants of Isaac's Bloodies. Cal disappointed that she won't be able to spend the day together with Reiji Sighs. But as Reiji leaves he says 'we have penalty of time, aren't we going to be together forever' Unknown to him, Lizzie is being used by the Godoh group to lure him out.

Reiji leaves The apartment, while Cal is disappointed Reiji promises he will return. Upon reaching the rendezvous, Reiji realizes it's a trap by Godoh and his men. When Reiji tries to convince Godoh of the misunderstanding, the yakuza leader believes that Claudia has tricked his gang. Godoh reveals that Claudia sent him and Shiga to steal the cocaine a year back. After the drug heist, Claudia's deal was to get Godoh's group to join Inferno. Godoh tells him that Claudia used all of them as chess pieces to further her own goals. Before anything else can happen, an unknown sniper attacks all of them. While the rest are killed or scattered, Reiji pursues the attacker and comes face to face with Elen. But Elen, now reverting to her Ein persona, warns him that Inferno will kill him before escaping. Godoh survives the attack and remembers Mio, his sister, who was separated from the family. As he makes plans to deal with Inferno, Shiga kills him to prove the Godoh group's loyalty to Inferno due to Scythe Master's manipulations. Lizzie goes to Claudia's mansion but finds it empty. Reiji plans to run away with Cal, but a bomb placed outside his apartment destroys it, leaving him to think that she died.

Reiji kills Inferno's men who bombed his apartment and makes his escape. Scythe Master and Shiga explain the whole situation to McGuire, pinning the betrayal on Claudia and Phantom. Claudia calls Reiji to tell him the reason of her betrayal and needs his help to escape. Elen goes to kill Reiji per Scythe's orders and Scythe reveals the next generation of assassins he's creating: the Zahlen Schwestern and reveals that Elen is no longer needed. Claudia and Lizzie meet up and drive to the beach, where Lizzie is forced to execute Claudia for her betrayal. Reiji returns to the desert warehouse and Elen arrives to kill him. After he persuades Elen to stop, the girl wants him to end her suffering. Reiji refuses to kill her and since he has a promise he is able to keep he would like to keep it. Elen decides to leave Scythe Master and Inferno and escape with Reiji. Lizzie visits Claudia and her brother Romero's graves. After getting fake Mexican passports, Reiji and Elen prepare to leave America.

The entire episode is a summary of Cal's life with Reiji with a few added scenes. While Reiji's apartment was bombed by Inferno's attack, Cal was actually out shopping in a store. For a few days, Cal remained in the apartment ruins waiting for Reiji to return but he never showed up again, since he's now on the run with Elen. Scythe Master appears to Cal and encourages her false belief that Reiji has abandoned her and broken his promise. Meanwhile, Reiji and Elen have headed to the outskirts of Mexico.

2 years have passed since Reiji and Elen escaped America and have settled themselves in a small town in Japan. They try to live out their lives normally and enroll in school. One day, Reiji is dragged by one of his classmates, Sanae, to meet her friend Mio Fujieda, who attempts to confess her feelings for him. After an awkward conversation, both of them agree to go on a date. During their date, Reiji and Mio encounter a biker who does a harmless sneak attack. Although Mio has no idea what's going on, Reiji is sure the biker is one of Inferno's men. Reiji and Elen have a discussion where Elen reveals that Mio's real surname is actually Godoh, which means she belongs to the yakuza family. Elen's intention is to be Mio's friend so that she can use her as leverage if Godoh and Inferno ever catch up to them. The pair begin to make plans for their escape. The next day, Reiji goes home from school and encounters the biker again, who produces a familiar pocket watch and plays its tune. To his shock, Reiji realizes the biker is none other than Cal, who is very much alive.

Reiji tells Elen that Cal is alive and is working for Inferno as an assassin, blaming himself for having introduced the girl into the underworld. Inferno helps the Godoh group dispose a rival Chinese mafia from establishing a foothold in the region. As the operatives begin to take action, Scythe sends in Cal to crash the mafias' meeting and kill all of them. Lizzie disapproves the way Scythe handled the situation. She is later told by Scythe that Cal, who now goes by the name of Drei, has to defeat the previous Phantom in order to attain the title. Reiji, Elen and their group of friends have lunch together, but Elen is called away after receiving an unknown package. Reiji loses track of her and instead encounters Scythe. Scythe thanks Reiji for providing him with Cal, who he uses to fan her hatred against him, and hints that Elen is being targeted. At the church, Cal introduces herself to Elen.

After exchanging formalities, Elen and Cal draw their weapons, leading to an even match between the two. Reiji arrives and tries to persuade Cal to end the standoff, but she refuses. The standoff ends when Lizzie interrupts and manages to convince Cal to leave. Lizzie lets Reiji and Elen go, but she warns them that Inferno won't let the pair off that easily. Reiji calls Shiga and threatens him using Mio to advise Inferno not to try anything. During her conversation with Lizzie, Cal reveals her dark thoughts and reasons for being an assassin. The next day, while Elen goes to negotiate their escape plans, Reiji and Mio go on a date again. While Mio is away, Cal appears to Reiji. He tells Cal that she can kill him on condition that she let Elen go. Cal states that she will make Reiji suffer before killing him. Later, Cal takes her frustration out on a group of thugs who get in her way.

Elen and Reiji resume their "normal lives" as students once more until Cal takes a personal visit to Mio. Telling her to ride with her, Cal meets up with Lizzie. However, she points her pistol at Cal and tells her to get away from Mio. After taunting Lizzie on whether she would really shoot her after taking out the pocket watch given to Cal by Reiji years ago when he held the codename Phantom by Inferno, Cal takes aim and shoots at Lizzie before driving away and leaving her to die. Reiji receives a phone message with threats from Cal. Meanwhile, Shiga visits Scythe and angrily yells at him for having dragged Mio into this mess after seeing the corpses of his men at the Mio residence. Scythe assures Shiga that he would take care of Cal himself, informing him that he had summoned reinforcements to take care of the problem.

Reiji tells Elen that he will handle Cal personally. Although Elen allows him to think about it, she leaves school early without informing Reiji. She then sends Reiji a voice mail, telling him to escape without her and she promises to catch up with him once she rescued Mio. Under captivity, Mio tries to convince Cal that Reiji isn't what she thought he was but Cal doesn't listen, However deep down, all Cal really wants is Reiji's love. Shiga reports Mio's kidnapping to old Godoh, her father and leader of the yakuza. He suggests having their retainers to intervene but her father chooses to let Inferno take care of the matter, preferring not to get too much attention with Mio. Scythe prepares to unleash his Zahlen Schwestern on Elen, Reiji and Cal. Cal calls Elen to meet for their duel and releases Mio. Elen arrives to Mio's location and reveals her and Reiji's true identities as assassins. She tells Mio that she won't be able to help Reiji. Mio feels helpless as Elen leaves to duel with Cal, while Reiji searches all over for Elen before she takes any action.

Mio's mother finally tells her the truth about her heritage and her father being alive, explaining that their separation was the only way to preserve happy memories together. Mio, realizing she feels this way about Reiji, calls to tell him about the duel between Cal and Elen and also says she will wait for him to return once he is happy. Cal arrives at the church to find Reiji there for the duel instead of Elen. Outside, Shiga and his men arrive to kill Elen, Reiji and Cal but are stopped and killed by Elen so they cannot interrupt the duel. Inside, the music ends and Reiji wins the duel, lethally wounding Cal. Crying, Reiji holds Cal as she dies and she finally releases her hatred and tells Reiji she is happy to be with him as she dies, since knowing and loving him were enough to give her life meaning. After Cal and Shiga's men are all dead, Scythe Master appears out of the shadows to begin the "finale of the play" he has written and releases the Zahlen Schwestern to kill Ein and Zwei.

Reiji and Elen defeat the Zahlen Schwestern after a difficult battle and Elen finally breaks free of Sythe Master's mental manipulations and is able to kill him. Meanwhile in America, Mr. McGuire is asked for his orders in regards to Phantom and muses over Ein and Zwei's accomplishments for Inferno. He states that youth must prevail over the old system and that Inferno must carry on; whether this means that Ein and Zwei are to be eliminated as part of the "old system" or to be retrieved as the "youth" is unknown. Six months later, Reiji and Elen have finally traced Elen's heritage back to Mongolia where they meet a dead end. While an old man tells Elen that you could never forget the sky of Mongolia; after finding a field to do so, Elen is content knowing this is her homeland and feels her journey is over. As Reiji watches Elen in the field, he vows that he will keep his promise to make Elen truly smile, which she does after finding peace through being with Reiji and finding her homeland. As a carriage passes by, a shot is fired; Reiji collapses to the ground. Elen is then shown unmoving while looking up at the sky; however a petal of a poisonous flower beside her, Oxytropis, is shown missing. The fate of Elen and Reiji is left unknown, leaving the ending ambiguous.