Hideyuki is killed on Kaori's birthday as he refuses to do a request for the head of a powerful crime syndicate. Ryo must avenge his death.

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.

In order to find out who is targeting a nurse who is due to be the recipient of a large inheritance, Ryo breaks his foot and ends up in the same hospital the nurse is staying. While Ryo must not tell the nurse that she is being targeted, he also finds out she does not have enough experience being a nurse.

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.

Ryo teams up with a beautiful American agent to find out who is smuggling tanks from Japan.

When Ryo is hired by Saeko to bait a well known assassin, the assassin takes notice and issues a formal challenge to Ryo.

A bride literally falls into Ryo's lap and along with it, some goons hired by the jilted groom. While trying to sneak up on her during the middle of the night, Ryo gets stung by an experimental, but deadly bee. The bride does have the antidote, but as Kaori finds out, it has "terrible" side effects, most notably showing the feminine side of City Hunter.

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.

Ryo's partner Hideyuki is frantic over the disappearance of her sister Kaori as a spate of abductions of women have swept Shinjuku. As he is trying to find his partner's sister, he comes across a man who is not who he seems to be. Together, they must find the secret into the kidnappings.

Ryo's client is a man who wants to fake his own death to be free from a powerful politician so he could be reunited with his daughter. The man admits to be spineless but he is more than meets the eye. Ryo must masquerade as the hitman not only to save his client, but to ensure that the men working for the politician do not bother his client again.

Ryo is requested to assist a female thief in stealing a black tulip from a fraudulent psychic. Kaori finds out that the psychic's butler has a crush on her and decides he may be helpful in obtaining the plant.

Ryo must protect a woman and a young boy from another country from being abducted by foreign agents. Kaori soon discovers that the young boy's actions and demeanor are exactly as Ryo's.

Saeko enlists the help of Ryo to solve the dissappearances of beautiful women in Shinjuku. The stakes are even higher when Kaori, mistaken for a beautiful woman, is also kidnapped. Ryo encounters the mastermind of the scheme, a supposedly beautiful woman who may not be who she seems to be.

When a father requests the services of City Hunter to protect his daughter from someone stalking her at work, he finds out that the stalker IS City Hunter. The father then requests that City Hunter convince her daughter to quit her job as he feels that she may be in danger of other stalkers. Ryo realizes that the young woman has lived a sheltered life and decides to teach her a few lessons in love.

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.

A new private investigation agency opens next door and it is run by Reika Nogami, Saeko Nogami's younger sister. While Ryo makes constant advances towards her, he learns about Reika's blackmail tactics against Yakuza gangsters as well as the death of her former partner. He also learns that someone has ordered a hit on Reika herself.

Reika explains to Ryo about how a corrupt police officer is interfering with narcotics investigations, and how her former partner was killed by the Yakuza and her desire to clear his name. This leads to a showdown against an expert marksman and also lands Ryo, Kaori, and Reika in Jail after being set up by the corrupt police officer.

Kaori has a recurring nightmare regarding Ryo's impending death. Meanwhile, Umibozu narrowly escapes death at the hands of three siblings who are powerful assassins hired by the Lodos Mafia. Badly shaken and wounded, Umibozu tries to find Ryo. At the same time, Saeko and Reika hire Ryo to help them bust a smuggling ring headed by the Lodos Mafia at a large masquerade. The three assassin siblings notice and decide to use this to their advantage. Their target: to kill Ryo by using Kaori Makimura as a hostage.

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.

Sophie Silverman is revealed to be the fiance of Robert Harrison and reveals her intentions of avenging his death. After seriously wounding Ryo, Sophie kidnaps Kaori as bait for a future showdown. While Ryo recovers from his injuries, he realizes that a syndicate known as the Guiness Corporation is after Sophie and had extorted Robert to take on a job that meant certain death at the hands of Ryo Saeba. When the Guiness Corporation ambushes Sophie and Ryo, the two put aside their rivalry to repel the attackers, only to find themselves in a deadly showdown.

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.