The story follows a small-time detective, his brother (who runs the business side of things), and two high school summer interns (nicknamed ManAya for the both of them). They get involved in a case where teenage girls burst into flames, turn to glass, then disintegrate. It is their duty to locate and protect one of these Glass Maidens, code name HW-9, from Kito and his organization.

Glass Maiden provides examples of the following tropes:

• Amazon Brigade: Tito's squad consists of grim-faced gunners.
• Camp Gay: Porilyn, large crossdresser who considers himself feminine.
• Cool Car: Shu's Pontiac Firebird Trans-Am.
• Cosplay Otaku Girl: Monica dresses up for Doc after hours.
• Deadpan Snarker: Ayaka is noted in-universe for speaking in a monotone.
• Genki Girl: Manami, with an unkempt head of orange hair and a motormouth.
• Gratuitous English (writing in OP and lyrics in the ED)
  OP: Never looking back ...I'll get started
  ED: Que sera-sera. All right! Don't take it too hard ... in this time ... Lonely hearts ...music ... Have a ball!
• In-Series Nickname: AyaMana = Ayaka + Manami
• Jazz: Both the OP and ED.
• Lovable Sex Maniac: Doc (Sensei) loves to spend after-hours filming Monica displaying sexy outfits.
• Mascot: Lil Q (Q-chan), the dog.
• Red Oni, Blue Oni: Manami, red to Ayaka's Blue.
• Surveillance Station Slacker: Porilyn's security room shows view from around (and outside) the city.
• Taken for Granite: Sara and the other Glass Maidens.

Characters

• Shu: Head of detective agency, the main protagonist, and an incorrigible lady's man.
• Akira: Shu's younger brother, is referred to as 'Mini-Boss'. His job is to bring in work for the company.
• Ayaka: Speaks in a monotone and is usually seen at her computer.
• Manami: Overenthusiastic assistant, wants to get credit as a detective, and is dominant in the ManAya pair.
• Sara: AKA HW-9, is the titular Glass Maiden. She can revert from glass to human and runs a consistantly high internal temperature.
• Porilyn: An effeminate man that is the source of many of the agency's assignments.
• Sophie: A disrespected reporter who knows more than what the police will admit.
• Doc: A competent but pervy doctor. His clinic is just below the detective agency.
• Monica: The sexy nurse, loves to cosplay for Doc.
• Kito: The chief antagonist and leader of an all woman brigade.
• BW-Alpha: A quiet girl who hides her true form which is ultimately fierce and dangerous.