Amia Riegl, known as 009-12, is a minor character in 009-1. She is part of the Nine Number Group, and exclusive to the anime adaptation. She is modeled after Cyborg 0012 from Cyborg 009, specifically the version of the character seen in the 2001 "Cyborg Soldier" adaptation. Her abilities were profiled in a booklet that came with the sixth Japanese DVD release. Within her description, she's described as the "biological computer" of the team and the smartest. From her brief holographic appearance, Amia appears as an incredibly pale-skinned woman with long, dark hair held back by a jeweled headband. Two front sections of her hair are tied off with white hair ties. She has no visible sclerae, and her eyes are a solid, sparkly black. In the present day, her avatar still seems to wear the blue Nine Number Group jumpsuit that is seen on the other cyborgs in the flashback sequence in the same episode. Through unknown circumstances, Amia Riegl became the very meeting room and intelligence system in the Zero Zero Organization, with her mind linked to the room and giving her the ability to project herself as a holographic secretary that existed within it. This would seem to prevent her from joining the rest of the team on their missions. While she exists as this hologram, her actual physical body remains frozen deep in a laboratory within the organization. She is noted as originating from somewhere in Northern Europe.

Vera Theremin, codenamed 009-11, is one of the twin operatives of the Nine Number Group in 009-1. She is the twin sister of Alyona Theremin (009-10), with the two being based on the twin cyborgs from Shōtarō Ishinomori's Cyborg 009. Both are associated with electrical abilities. Vera appears only briefly in the final episode of the 2006 anime and receives very little individual characterization. As a result, there is limited established information about her personality, background, or specific abilities beyond her connection to Alyona. She is identified by the designation 009-11, while her twin carries 009-10.

Alyona Theremin, codenamed 009-10, is one of the twin operatives of the Nine Number Group in 009-1. She works alongside her twin sister, Vera Theremin (009-11), as part of the Western Bloc's intelligence organization. The sisters are based on the 0010 Plus and Minus twins from Cyborg 009, and both possess electrical abilities. Alyona and Vera are among the less-developed members of the Nine Number Group. In the 2006 anime, they appear briefly without dialogue, including in the group's flashback and near the end of the series. Alyona is identified by the designation 009-10, while her twin carries the designation 009-11.

Mio Murashima, codenamed 009-9, is an operative of the Nine Number Group in 009-1. She serves the Western Bloc's Zero Zero Organization as one of the numbered agents assigned to covert intelligence work. Unlike several of her teammates, Mio receives very little individual development or dialogue in the 2006 anime, making her one of the more enigmatic members of the group. Her designation, 009-9, places her among the twelve female agents of the anime's Nine Number Group. The name "Mio Murashima" may be an intentional reference to Joe Shimamura, the central character of Shōtarō Ishinomori's Cyborg 009. Mio is therefore best characterized as a largely unexplored member of the organization rather than assigning her abilities or personality traits that are not established in the available material.

Una Barry, codenamed 009-8, is an operative of the Nine Number Group in 009-1. Working for the Western Bloc's Zero Zero Organization, Una is one of the specialized agents assigned to covert intelligence operations during the conflict between the Eastern and Western Blocs. Her distinctive cybernetic ability is underwater breathing, allowing her to operate in aquatic environments without relying on conventional breathing equipment. Una is one of the more briefly explored members of the Nine Number Group in the 2006 anime, with much of the information about her coming from supplementary character material rather than extensive on-screen appearances. She is identified by the designation 009-8.

Mia Connery, known as 009-7, is one of the prominent cyborg agents shown in the 009-1 series. She is part of the Nine Number Group, and exclusive to the anime adaptation. She is modeled after Great Britain/007 from Cyborg 009. Mia is a shape-shifting cyborg, with the ability to transform into whatever she can put her mind to. Her backstory was briefly detailed in an extra booklet that came with the sixth DVD release in Japan. In the manga, a different 009-7 appears. This agent resembles Mylene, but with slightly darker hair, and has enhanced vision and hearing. She is soon killed on her mission. Although Mia was a talented theatre actress, she found herself unlucky. She brought her theatrical talent to the Zero Zero Organization for a small mission, and proceeded to join them without full knowledge of the role that she would be getting herself into as an agent.

Fei Chang, codenamed Agent 009-6, is a character in 009-1. She is a secret agent of the all-female Nine Number Group, one of the ten groups in the Zero Zero Organization, a Western Bloc intelligence organization. Fei is a cybernetic agent who works alongside Mylene Hoffman (009-1), Judy Moore (009-2), Salma Banderas (009-5), and the other members of the Nine Number Group. Like the organization's other operatives, she has received cybernetic modifications that enhance her capabilities as a secret agent. As a member of the Nine Number Group, Fei participates in missions involving espionage, infiltration, intelligence gathering, and conflicts between the Eastern and Western Blocs. Fei operates under the codename 009-6, carrying out assignments for the Zero Zero Organization as a trained intelligence operative.

Salma Banderas codenamed Agent 009-5, is a character in 009-1. She is a secret agent of the all-female Nine Number Group, one of the ten groups in the Zero Zero Organization, a Western Bloc intelligence organization. Salma is a highly capable cybernetic agent who serves alongside Mylene Hoffman (009-1), Judy Moore (009-2), and the other members of the Nine Number Group. Like the organization's other agents, she possesses cybernetic enhancements that support her abilities as an intelligence operative. As a member of the Nine Number Group, Salma takes part in missions involving espionage, infiltration, intelligence gathering, and conflicts between the Eastern and Western Blocs. Salma operates under the codename 009-5, carrying out assignments for the Zero Zero Organization as a trained and experienced secret agent.

Berta Kästner, known as 009-4, is one of the prominent cyborg agents shown in the 009-1 series. She is part of the Nine Number Group, and exclusive to the anime adaptation. She is modeled after Albert Heinrich/004 from Cyborg 009. Berta is a specialized combat cyborg and "human weapon", with built-in firearms and ammunition stored throughout her body. Her backstory was briefly detailed in the extra booklet that came with the sixth DVD release in Japan. Berta was a child of poor immigrants, but rose to greatness in becoming a highly-active athlete. However, she was soon seriously injured in a traffic accident. The Zero Zero Organization offered to reconstruct her limbs with cybernetic surgery, with the condition that she join them as one of their intelligence agents.

Vanessa Ibert, known as 009-3, is one of the prominent cyborg agents shown in the 009-1 series. She is part of the Nine Number Group, and exclusive to the anime adaptation. She is modeled after Francoise Arnoul/003 from Cyborg 009. Vanessa, along with Berta (009-4) and Mia (009-7), gets to do the most on missions with her leader. She acts as a reconnaissance cyborg, with specialized vision and hearing that allows her to see and hear from far distances. Her eyes also act as cameras. Her backstory was briefly detailed in the extra booklet that came with the sixth DVD release in Japan. Vanessa was a privileged to be in a wealthy upbringing, with great plans to become a pianist in her future. However, her happiness was cut short when her family was killed as a result of terrorism. She was then brought into the Zero Zero Organization, in circumstances that were similar to Mylene's.

Judy Moore, codenamed Agent 009-2, is a recurring character in 009-1. She is a secret agent of the all-female Nine Number Group, one of the ten groups in the Zero Zero Organization, a Western Bloc intelligence organization. Judy is a skilled cybernetic agent who works alongside Mylene Hoffman (009-1) and the other female agents of the Nine Number Group. Like the other members of the organization, she has undergone cybernetic modifications that enhance her abilities and make her an effective intelligence operative. Judy is known for her professional attitude and experience as a member of the Nine Number Group. She participates in missions involving espionage, infiltration, intelligence gathering, and conflicts between the Eastern and Western Blocs. As an agent of the Zero Zero Organization, Judy operates under various assignments and identities as required by her missions. She is primarily identified by her codename, 009-2, and is known as Judy Moore.

Mylene Hoffman, codenamed Agent 009-1, is the titular protagonist of 009-1. She is a secret agent of the all-female Nine Number Group, one of the ten groups in the Zero Zero Organization, a Western Bloc intelligence organization. She was orphaned at an early age, after her family got caught up in the midst of a battle between the Eastern and Western Blocs. Her parents died and was separated from her brother Paul, who she believed had died in the crossfire as well. She was then taken away by soldiers of the Western Bloc and was raised as an intelligence agent, hoping to find the faction that killed her family though at times she subconsciously cannot perceive those around her. Per protocol, Mylene goes through various aliases, including "Miss Nine", "Cool Liz", "Lily Lam", "Mylene Duke", and "Melinda Pierce", while she goes by "Muse" in the anime.

Aki Yoshimoto is the transgender kid of Ken'ichi Yoshimoto and Aya Toyomori's child. Aki inherited Ken'ichi's straightforward confidence and Aya's playful personality. They're usually friendly and easy to talk to, but they can become surprisingly determined when something matters to them. They're also somewhat thoughtful beneath their energetic exterior. Aki likes figuring things out independently and doesn't appreciate being treated differently simply because they're transgender.Aki grew up knowing that their parents supported them. Coming out as transgender was an important part of understanding themselves, and they gradually became comfortable being open about who they are.

Seiji Tokuzawa is a supporting character in the adult visual novel adaptation Chijoku no Seifuku (also known as Uniform of Disgrace). Seiji is the husband of Akemi Tokuzawa. As a busy professional, his frequent absences and preoccupation with work leave his wife isolated at home. This situation is exploited by their young neighbor, Ken'ichi Yoshimoto, who uses covert surveillance technology to monitor the household and seduce Akemi.

Ken'ichi Yoshimoto is the primary protagonist of the adult visual novel adaptation Chijoku no Seifuku (also known as Uniform of Disgrace). Ken'ichi is a tech-savvy young man who uses hidden surveillance technology to monitor and manipulate those around him. After successfully winning over his married neighbor, Akemi Tokuzawa, Ken'ichi sets his sights on Kasumi Ogawa and Aya Toyomori. By secretly recording and gathering leverage on them through video surveillance, he schemes to force them into submitting to his desires.

Mitsuhashi Serika is a former classmate of the protagonist, she is now a flight attendant who reunited with the protagonist at the airport where she works.She boasts an outstanding beauty comparable to that of a foreigner. Because of her appearance, she became a queen-like character.One the surface, she is amiable, but on the inside, she is self-centered and always looking down on others.When they were students, she always bullied and humiliated the protagonist.Even after reunion, she vents the stress of the job by bullying him every time they face each other.The protagonist considered her a loathsome opponent. An enemy to be overcome and conquered.

Narita Hina is the younger sister to Akemi. She is a student at a school in the local neighborhood and works part-time in her family's restaurant.She lives with her parents, but when Akemi's husband isn't around, she often comes over to stay with her sister. Hina is a reliable person who helps out her sister, who is a bit slow.She has a cheerful personality and is uninhibited for her age. But her innocent words can sometime hurt others. She reminds the protagonist of his horrible student days. She in turns is suspicious whenever he approaches Akemi.

Tokuzawa Akemi is a beautiful young wife who resides in the same apartment building as the main character, leading to frequent everyday interactions. She is a dedicated homemaker with a ladylike, kind, and gentle disposition, possessing a modest and quiet personality. Because she leads a fairly sheltered life, she exhibits an innocent and trusting nature, often unaware of how naive she can appear to others. She shares a deeply loving bond with her husband, who travels frequently for business; the two always celebrate his return by preparing special dinners together and cherishing their quality time. For the protagonist, she serves as a warm, welcoming neighbor and a comforting, aspirational presence in his daily life. She ultimately becomes a mentor figure who inspires his curiosity and helps lay the foundation for his interest in storytelling and observational character study.

Toyomori Aya is a nurse at the hospital where the protagonist's friend is admitted. Although she graduated from nursing school with top grades, she has a friendly and humble personality. She is a bit headstrong and will not be intimidated by anyone when speaking up for what is right. ​She is trusted by those around her and is affectionately referred to as the "Shadow Director" for her natural leadership. Due to attending an all-girls school, she is not very experienced with social dynamics outside of her familiar circles, and she sometimes worries that her straightforward nature makes her seem unapproachable. Similar to Akemi, her dedication inspires the protagonist, who hopes to earn her respect and learn from her strong work ethic.

Ogawa Kasumi is a soft-spoken woman working in a department store. She has a calm and ladylike personality that exudes an air of innocence. She is appreciated for her work ethic and is loved by those around her. Although she avoids telling anyone, she has a very strong passion for baking, and has all sorts of professional kitchen gadgets in her possession. Although she longs to open her own bakery someday, she is embarrassed by how overly enthusiastic she gets about pastries and keeps her creations to herself. In spite of her sweet tooth, she remains mindful of health and only uses wholesome, organic ingredients. She buys beautiful vintage cake stands and practices decorating elaborate desserts while displaying them...