14 year old assassin code named Glass Heart from the Suzacu unit doesn't want to kill anymore. Every time she kills her heart breaks and all she wants is to break free. Will her answer to her problems be the right one and solve all her problems like she wants. She’s not a lost cause yet and one year later Glass Heart is about to learn what her heart truly wants. Meanwhile somewhere else another broken heart wonders the streets. After an accident his fiance was involved in one year ago he wonders if his life will ever be the same.

Given a new chance to live Glass Heart escapes from the surgery and decides to seek the meanings of her visions. She must find Saeba Ryo but when she gets to Shinjuku she finds it hard to leave old habits like killing behind as her heart is not made of glass anymore. Will she find what she is seeking without losing herself in memories that dont belong to her and the places which are familiar to a part of her but she has never been to.

Upon hearing Umibozu's statement that Kaori has returned, Saeba Ryo prowls the streets of Shinjuku, aimlessly looking for Kaori. At the same time, Glass Heart, with a whole-hearted desire to meet Ryo, uncovers clues about the secret message board code "XYZ" to contact City Hunter. She goes to the location of the message board at Shinjuku Station guided by visions of Kaori, however the board has been removed because it is no longer used. Glass Heart loses hope of meeting City Hunter and faints, but before she hits the ground, Ryo arrives and catches her, then takes her to a local clinic.

After recovering consciousness in the clinic, Glass Heart has an encounter with Kaori in a mirror, which sparks a feeling in Glass Heart that her mind and body are being usurped by Kaori, creating hostility towards her heart donor. Witnessing this, Doc, the doctor, goes to Umibozu's cafe where he tells Ryo, Umibozu and Superintendent Saeko Nogami that the girl with Kaori's heart also has her memories. Meanwhile, Li Jian Qiang, the boss of Zheng Dao Hui has secretly arrived Japan and is being briefed by Mochiyama on Glass Heart's appearance in Shinjuku when Li is shot in the head by a sniper. Mochiyama recalls that Glass Heart was searching for City Hunter and meets him to warn him that the assassin is after him, hoping for them to eliminate each other. However, after seeing her photo, Ryo realizes that Glass Heart is the one with Kaori's transplanted heart. Meanwhile Glass Heart retrieves a weapons cache.

Li Jian Qiang, the boss of Zheng Dao Hui, was critically wounded in the assassination attempt. Saeko, the superintendent of Shinjuku West police station, sets up an emergency response headquarters because of the potential power vacuum in the Shinjuku gangland if Li dies. Glass Heart, who is assumed to be the assassin, becomes the prime target of the Zheng Dao Hui, who aggressively search for her in the streets of Shinjuku. Meanwhile, Glass Heart, has lost her identity and reason to live, and prepares to shoot herself in her heart, but Kaori's influence stops her from pulling the trigger. Me awhile, Master Li visits Umibozu's café and appears before Ryo who realizes that the person shot was Li's secret double, his twin brother, Li Qian De.

Ryo recalls the time, 22 years ago, when he rescued Li Qian De from a country's guerrillas on the request of his twin brother Li Jian Qiang. Ryo visits the Zheng Dao Hui medical facility where he recognizes Qian De and says goodbye to him as he takes his last breath. Back in Umibozu's café, Li Jian Qiang, explains to Ryo that Glass Heart is his long lost daughter Xiang-Ying who had attempted suicide, and confesses that Kaori's Heart was stolen in order to save her without him knowing its origin. Later, Glass Heart finds her way to the café, and emotionally meets Ryo, face-to-face for the first time.

Glass Heart becomes acquainted with Ryo in Umibozu's café, but the Qing Long, the infantry branch of Zheng Dao Hui led by Zhao, are close behind. The two manage to escape and lead the soldiers of Qing Long through the locked down the streets of Kabukichou area in Shinjuku. As they are chased, Glass Heart tells Ryo to save himself and kill her, but he replies that she has been given a second chance to live which she should cherish. Ryo communicates with Saeko through the city surveillance system and offers to lead the pursuers to a hotel in a deserted area where the Special Assault Team (SAT) can engages them without endangering the citizens.

In preparation for the gunfight with Qing Long, Ryo takes Glass Heart into a district that is blockaded off, and they finally reached the Hotel Kojyo. Waiting for them there is a large group of Ryo's friends including Umibozu, Saeko and Doc in the midst of a party. They intended to fight along Ryo against Qing Long which Glass Heart cannot comprehend, as she was trained to never rely on anyone. As the showdown draws near they all drink a toast to Kaori. Meanwhile a scout from Qing Long has infiltrated the building, and Glass Heart goes to engage him by herself. However the man turns out to be Liu Xin Hong who she knew only as Number 36, and she was known as Number 27, while training for Zheng Dao Hui. He was her only friend, but she thought she had killed him in the final trials for the Suzaka Unit. After declaring his love for her, Xin Hong leaves to set off a massive explosion in the Qing Long headquarters to protect her, but he is saved from death by Ryo.

While unconscious, Liu Xin Hong recalls his training days, when he and Number 27 trusted and supported each other, but they were forced to fight to the death in the final test when Number 27 thought that she had killed him. When he regains consciousness, he reveals that he was the sniper who had shot Master Li, but he only stayed alive to see Number 27 again. Meanwhile, another branch of Zheng Dao Hui fills the area with sleeping gas, and abducts Xin Hong. Barely awake, Glass Heart stabs herself to keep awake and goes after Xin Hong's captors. Master Li questions Xin Hong who says the was hired to assassinate Li by Zhao and that he chose to leave his unit and join Glass Heart because he owes her his life, unaware that she is Li’s daughter. Li ritually "executes" him for his rebellious action and then allows Xin Hong to leave the organization. Master Li's personal bodyguard, the Genbu unit, are sent to finish off the traitorous Zhau and Qing Long. Glass Heart finds Xin Hong just before falling unconscious, but he leave for some unfinished business while Master Li has a tearful reunion with his daughter, Xiang Ying.

Master Li is reunited with his unconscious daughter Xing Hong, now known as Glass Heart. Li decides to liquidate Cho, one of his ambitious lieutenants, who was behind the assassination attempt and who ordered the Qing Long unit to kill Glass Heart. Genbu and Xin Hong race to kill Cho but Xin Hong is stopped by Grand Chamberlain Chen, Master Li's right-hand man to allow Genbu to punish Cho, however he is sniped first by Ryo. Ryo reveals Glass Heart's real name, Xiang Ying, to Xin Hong and suggests that Xin Hong should be the one to tell her. Xin Hong later finds out that she is also Master Li's daughter. While unconscious, Glass Heart again communicates with Kaori about her relationship with Ryo whom she sees as a father figure. When Glass Heart awakes, she calls Ryo "papa" and later asks him to be her father. Ryo accepts, realizing that she is the child that he and Kaori could never have.

Xin Hong loses his confidence at the last second and decides not to tell Glass Heart her real name, but he accidentally says "Xiang Ying". Embarrassed, he tells her that Ryo made up the name and she accepts it. Ryo arranges for Xiang Ying to show Master Li around Shinjuku, without revealing that Li is her father. Li and Xiang Ying ended up taking pictures together at a photo booth, and when the photos are printed out, they realize they are both wearing the same expression.

Ryo and Xiang Ying attended the funeral of Qian De, who was her uncle. Jian Qiang tells Ryo how he met Xiang Ying's mother, Lin Xiang Ping, and how it was his caring brother Qian De who brought them together and encouraged him to have children. Although he lived in his brother's shadow Qian De was happy to be out of the limelight, and especially enjoyed that Xiang Ying thought that she had two fathers. As Qian De's ashes are scattered on the ocean, Xiang Ying asks Ryo to scatter her ashes on the ocean if she dies before him.

Ryo and Xiang Ying adjust to life together and she insists that Ryo undergo a medical exam and he is pronounced healthy. When Xiang Ying also undergoes an examination, it is discovered that there is an unusually high level of compatibility between her and Kaori indicating that her heart is unlikely to be rejected and that she may outlive Ryo, to her great relief. Later, Chen, Master Li's right hand man, shows Ryo a new ornate message board in Shinjuku Station with the words "XYZ: Be a good father - Li" and Ryo decides to start up his City Hunter business again.