When two brothers make an attempt on Ryo's Life, Kaori pushes Ryo out of the way only to suffer a head injury and amnesia as a result. Ryo realizes that he himself may be responsible for Kaori's predicament, so he makes arrangements for her to start a new life outside the underworld.

Humiliated in their last encounter, the Silver Fox pledges revenge against Ryo. He issues a formal challenge to Ryo by saying that he has targeted Kaori, Ryo's "lover" for death and that Ryo must protect her from his attacks. When Kaori confronts Ryo about this, Ryo acts non-commital to the challenge. After an incident in which Ryo falls for a trick set up by the Silver fox, he informs Kaori that she is no longer to be his assistant.

General Jimetil, formerly of the Pamela Republic, flies to Tokyo as an exile. At the same time, his personal guard tries to make a strike against Ryo in order to acquire Misa as a stake against her father. While they are unsuccessful in trying to kidnap Misa, they are able to grab Saeko. Ryo must attempt to try to save Saeko without sacrificing Misa's safety.

After Ryo, Saeko, and Umibozu are able to thwart an ambush set up by Sarah, her group, the Black Army, makes a ransom demand to the Japanese government with the threat of blowing up a nuclear bomb in the heart of Shinjuku. With the information on their hideout from Rumi, Ryo decides to take the Black army on. But when he realizes the truth of Sarah's identity, he finds that he is unable to shoot her.

After helping to protect a young girl named Akemi from some ruthless thugs, she insists that Ryo is her future husband and that they were destined to be married. While Ryo is able to get away, Akemi decides to enlist his help as her bodyguard to protect her from an unknown assailant named Kaijin X. In fact, the marriage story is a farce so that Akemi can leave her career as a young model.

Kaori seeks hiding from the Silver Fox with Umibozu. She then catches Ryo babbling to Saeko babbling about how Kaori is just crazy about him and how he does not really care about her and that Kaori is unfit to be Ryo's partner (even though Ryo really cares for Kaori). With that revelation, she seeks training in creating boobytraps from Umibozu and seeks to take matters in her own hands by challenging the Silver Fox herself.

It turns out that the document that Ookouchi is looking for is not the land ownership certificate, but a black leather pocketbook which is a ledger for Ookouchi's shady dealings. Also, Hitayoshi reveals why he is under Ookouchi's thumb, he unknowingly assisted in Ookouchi's criminal activities by allowing him to illegally plunder goods and resources sent to Japan after World War II. Ookouchi requests an exchange: the pocketbook for the kidnapped girl, but Ookouchi has a trap laid out for them as well as razing Kusunoki House to the ground.

Ryo notices that he is being watched by Kozue, a 12 year old girl confined to a wheelchair. When he pays her a visit, Kozue remarks that he is the second person to notice her, the first being a mysterious man with a beard. Kaori suspects that Ryo is using Kozue to get to her much older sister. But when the mysterious man attacks Kozue, Ryo decides to have Kozue and her sister live with him until he can figure out what is going on.

Kozue begins to enjoy life with Ryo and decides to try to set him up with her older sister. Meanwhile, Ryo finds out that Kozue was wounded by an unknown man who had killed another over a deal gone bad, and the bullet stuck against her spine is the cause of her paralysis. The arrival of Detectives Iwadate and Saeko also begins to complicate matters. With Kozue scheduled to undergo an operation which may allow her to walk again, Ryo realizes that Kozue may be in greater danger than initially thought.

Ryo discovers that Akemi is being targeted by a professional assassin named the Silver Fox. Ryo must protect her while helping her get out of a career in entertainment.

Ryo and Saeko's date is interrupted by the discovery of a known fraud, and the subsequent traffic stop by a beautiful traffic cop. Meanwhile, Kaori finds that she was ripped off into buying a fake designer fur coat. The traffic cop then decides to help Ryo find the fraudster, whom is also the suspect Saeko is after.

Kaori tries to convince Ryo to find Salina (who is really Princess Alma). But when the real Salina is kidnapped by the perpetrators, Ryo, still unaware of the identity switch, must save her from the trap that the perpetrators have planned, all this while protecting the real Princess Alma.

Despite suffering numerous injuries, Umibozu disappears to take on Dandy Jack, who was responsible for the death of his former partner who was Kathleen's father. Kathleen goes back to Dandy Jack's chateau, not knowing that she is being used in Dandy Jack's revenge against Umibozu. Once at Dandy Jack's chateau, Dandy Jack spots Umibozu and creates a scenario for a showdown between Umibozu and Kathleen.

An airliner is hijacked and all of the women are being held captive. After assisting in dealing with the hijackers, Ryo makes off with Misa Williams, unaware that she is the daughter of the leader of the opposition in the Pamela Republic. Saeko, hired to guard Misa by General Jimetil, ruler of the Pamela Republic, gives chase along with Kaori. After intercepting Ryo and Misa at a bathhouse where Ryo has taken care of two men trying to kidnap Misa, Saeko informs them that General Jimetil has been overthrown by the opposition.

Yoko is furious about the drug bust and realizes that the City Hunter was involved. While on a search at the scene, she is accosted by members of the Unryu-Kai gang who have a grudge against Ryo and realizes this is the best opportunity to have an interview with the City Hunter.

Ryo suspects that Interpol Agent Nelson may in fact be in league with the revived Red Pegasus drug cartel. After a boat chase, the information of the drug smuggling route is revealed, the route ends at an orphanage that Hideyuki visited shortly before his death, and that a postcard addressed to him from the orphanage was meant to lead Kaori to that location.

While doing research for a hardcore mystery novel, the publishing company sends a bodyguard to guard Azusa while she completes her book. Her adventures include visiting friendly Yakuza, an interview with Umibozu, and a plot to kill the friendly Yakuza boss. What she does not realize is that the City Hunter is the bodyguard hired to protect her.

After stealing a supposed forgery of a masterpiece, the daughter of a famed artist requests Ryo's services to help her expose her father's former protege as a fraud.

Umibozu asks Ryo to take care of a young American girl named Kathleen Heywood. However, Ryo realizes that Kathleen is actually out to kill Umibozu in revenge for her father's death. The Arrival of known mercenary Dandy Jack complicates matters, and Ryo realizes that he may be the one who is manipulating Kathleen.

Ryo decides to take on Saeko's request to assist a not-so-beautiful female police officer in training for an Olympic event. Ryo realizes the young officer is being targeted by a man with a grudge, while deciding to take the officer to get a makeover to unlock her "true beauty".

Ryo meets Yoko Fuyuno, a reporter intent in writing a story about the exploits of the City Hunter. Ryo realizes that if Yoko writes her story, his cover would be blown, so he tries many ways to convince her to not write the story, starting from the fact that he is Ryoji, Ryo's fictional younger brother. A request from Saeko to bust a drug transportation route complicates matters so Ryo goes through extreme measures to bust the route while not attracting suspicion from Yoko.

After a Shooting Range accident, Ryo finds out that Keiichi and Keiko are in fact the same person. But Ryo decides to hide this fact from Kaori. When Ryo makes advances towards Keiko while she is in his male costume, Kaori is furious thinking that Ryo would rather be attracted to a man rather than her. Kaori is then kidnapped by the man attempting to kill Keiko and Ryo and Keiko must rescue her.

Nelson, an Interpol Agent approaches Kaori over allegations that Kaori's deceased brother had smuggled drugs and hidden information regarding a drug smuggling route. The accusations against Hideyuki pile up when Saeko is also assigned to the case. The Red Pegasus returns with a plot to gain vengeance against Ryo and Kaori, but Umibozu is able to save the two from being abducted by the re-energized drug cartel.

Ryo's client is a young girl with a unique telepathic ability to read minds. However, Ryo is smitten by the girl's nanny, a woman with martial arts skills. The young girl, Sara, is entranced by Ryo and his abilities, despite the fact that his mind is filled with "Mokkori" most of the time. It turns out that Sara is the only daughter of the head of a large family conglomerate and that many of her relatives are after her. Sara also runs into a disturbing fact: that Kaori is secretly in love with Ryo.

While shopping for dates, Ryo comes across a young woman who decides to parade him in front of her country-living father in order to convince her father that she is seeing someone and wants to stay in the city. When her father notices that Ryo has a gun, Ryo tries to pretend to be a police detective, steals a police car, and promptly gets involved in trying to break up a hostage situation during a bank robbery.