When there is a spate of random shootings in Shinjuku, a sister of one of the victims wants Ryo to catch the killer and bring him to justice. But Ryo can tell that there is much more than justice that his client is interested in.

Ryo's client is a daughter of a known scientist who developed a deadly microbe that could render humanity sterile. His client wants him to protect her at all costs while she develops a vaccine, but should she be captured, she wants him to kill her before terrorists can extract the knowledge of the microbe from her.

Umibozu returns to ask Ryo to help him protect Maki, the daughter of his old mentor. Ryo learns of the story of Daddy Longlegs and that Umibozu has been supporting her from a distance. Ryo pretends to take Umibozu's place and then tries many opportunities to sleep with Maki.

Ryo and Kaori come across two opposing jobs involving the same people. Kaori is hired by a member of a Biker Gang who wants her to pretend to be his girlfriend in order to deflect attention from the daughter of a tycoon. And Ryo is hired by the daughter to convince the biker to leave his gang and live a normal life.

Umibozu is injured while protecting a female pianist with whom he has affection for. He enlists the help of Ryo to help protect the girl from a corrupt politician involved in a bribery scandal and who is trying to report the story in honour of her dead fiance.

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 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.

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.

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.

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.

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".