A 15-year-old girl, code-named "Glass Heart", who has been trained as a killing machine by the Taiwanese mafia, attempted suicide. After receiving a heart transplant, she lives and remains in a coma for a year. On the other hand, a year ago, a sweeper known as Saeba Ryo, AKA City Hunter, lost his beloved partner, Kaori Makimura, to a car accident. Ever since then Ryo has lived an idle life and believes that Kaori thrives on elsewhere after her death despite not knowing to whom it's borne.
Episode 2: Kaori's Return 『香が帰ってきた』
After finally regaining consciousness, Glass Heart fled from the organization and aimed for Shinjuku, as led by Kaoru and Ryo in a dream. While standing at the intersection of an unfamiliar Shinjuku, she heard a voice from within saying “I died here”. That was where Kaoru died. However, being entangled with the yakuza and chased by the police, a car explosion ensued. Also, as if led by someone, she ended up at Cat's Eye café run by Umibozu, a friend of Ryo. There, a blind Umibozu felt the return of Kaoru.
Episode 3: The Streets of XYZ 『ＸＹＺの街』
After hearing from Umibozu about the return of Kaoru, Ryo wandered the streets of Shinjuku in pursuit of 'her'. Around that time, while wanting to meet Ryo, Glass Heart stumbled upon the mystery of XYZ; which was, if a message was left on a message board at Shinjuku Station, one would get to meet City Hunter Ryo Saeba. Led by a vision of Kaoru, she searched for the message board.
Episode 4: Wandering Heart 『さまようＨＥＡＲＴ』
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Episode 5: Goodbye Kaori 『永別（さよなら）…カオリ』
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Episode 6: Reunion 『再会』
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Episode 7: My Beloved City 『俺の愛すべき街』
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Episode 8: True Friends 『真実（ホント）の仲間』
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Episode 9: Lost Name ~Xiang Ying~ 『香瑩～失われた名前～ 』
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Episode 10: Angel Smile 『エンジェルスマイル』
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Episode 11: A Time For The Father And Daughter 『父娘（おやこ）の時間』
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Episode 12: An Encounter And Farewell On Board A Ship 『船上の出会いと別れ』
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Episode 13: A Gift From Chief Li 『李大人からの贈り物』
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Episode 14: City Hunter's Revival! 『復活C・H（シティーハンター）!』
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Episode 15: Looking For Papa! 『パパを捜して！』
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Episode 16: A City Hunter's Qualification 『Ｃ・Ｈ（シティー・ハンター）としての資格』
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Episode 17: A Meeting In The Dream 『夢の中の出会い』
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Episode 18: The Bond Between A Parent And The Child 『親子の絆』
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Episode 19: Old Chief Chen's Shop 『陳老人の店』
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Episode 20: Fate's Prelude 『宿命のプレリュード』
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Episode 21: Sorrowful Guardian 『哀しき守護者（ガーディアン）』
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Episode 22: Unfair Happiness 『不公平な幸せ』
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Episode 23: Melody of a Journey's Beginning 『出発（たびだち）のメロディー』
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Episode 24: Together With The Beat... 『鼓動と共に……』
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Episode 25: A Client's Death Wish 『死にたがる依頼者』
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Episode 26: Once Again, To That Moment 『もう一度あの頃に』
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Episode 27: Me, In love!? 『私、恋してる！？』
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Episode 28: The Promise 『約束』
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Episode 29: My Younger Sister...Kaori 『私の妹・・・香』
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Episode 30: This City is Everything to Me 『この街は私の全て』
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Episode 31: Miracle On The Last Night 『最後の夜に見た奇跡』
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Episode 32: The Girl From The Organization 『組織から来た女』
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Episode 33: The Child Who Is A Gift From God 『神から授かりし子』
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Episode 34: Two's Determination 『二人の決意』
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Episode 35: Towards The Future 『未来へ…』
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Episode 36: The Girl That Brings Happiness 『幸せを運ぶ女の子』
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Episode 37: Untainted Heart 『汚れのない心』
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Episode 38: Be My Eyes 『オレの目になってくれ』
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Episode 39: The Client Is A Famous Actress 『依頼者は大女優』
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Episode 40: Miki's Hidden Secret 『ミキの隠された秘密』
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Episode 41: The Place Where I Belong 『自分の居場所』
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Episode 42: The Sign That Only The Two Knows 『二人だけのサイン』
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Episode 43: A Day In My Life 『私が生きる日常』
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Episode 44: For Our Children 『俺たちの子供のために』
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Episode 45: The Human Nuclear Warhead, Yang 『人間核弾頭、楊（ヤン）』
