In 1992, Momiji Fujimiya is a middle school student living with her mother and grandmother in the city of Izumo, Shimane. One day, she is confronted on her way to school by a cat-eyed man with blue magatama beads embedded in his hands, who attempts to kill her. He refers to her as Kushinada. Momiji is saved by the sudden appearance of two government officials, one of whom shoots the man in the arm and sends him fleeing.

Momiji is intrigued as to why she was referred to as the Kushinada. She discovers that the Kushinada refers to an ancient princess whose blood holds the power to stop the ancient monsters known as Aragami by sending them to an eternal sleep. Momiji dismisses the idea that she could be such a person, but reconsiders after vines begin to appear from every crack and opening attempting to capture her.

Momiji tries to escape, not knowing that the vines are being employed by a powerful Aragami known as the Yamata no Orochi. She is saved by the man with the magatamas embedded into his hands, who introduces himself as Mamoru Kusanagi. He confronts Orochi using Momiji as bait. The plan fails and the government officials appear again. They reveal themselves to be members of the Terrestrial Administration Center (TAC for short), and subdue Orochi. However, with the last of its strength, it attacks Kusanagi.

Momiji saves Kusanagi by taking Orochi's blow. Impaled by the Aragami, instead of dying, she is instead fused with the magatama, more specifically identified as a mitama, which gives Momiji the ability to sense the presence of other Aragami. The TAC agents explain that they are an organization dedicated to defeating the Aragami, who seek to destroy humanity. The current Kushinada, Momiji, must aid them because the other Kushinada, Momiji's twin sister Kaede Kunikida, is now dead. Momiji, wishing to discover more about the twin sister she never knew and also to fulfill her destiny, agrees to join the TAC under the protection of Kusanagi, who wishes to destroy his former masters, the Aragami.

Kusanagi repeatedly attempts to kill Murakumo, a man with eight mitamas who kills any renegade Aragami. Kaede reappears along with a strange energy field in Tokyo. Murakumo and Kaede intend to resurrect the god Susanoo and purify the world of humanity's influences, with Kaede acting as the leader of the movement.

There is also a three episode OVA, Blue Seed Beyond, which takes place two years after the end of the TV series. It concerns what seems to be a resurgence of aragami (actually created via biotechnology), and introduces a new character, Valencia Tachibana. Like Kusanagi, she was implanted with a mitama without turning into a full aragami.

• Momiji Fujimiya (藤宮 紅葉, Fujimiya Momiji): Momiji is the descendant of the "Kushinada". She lives in Izumo, where Princess Kushinada lived. An eighth-grade student, she was unprepared to understand her destiny to battle the Aragami. She becomes a member of the TAC in order to stop the Aragami from destroying humanity. An ironic twist of fate has Momiji carrying a mitama – an Aragami "soul" – embedded in her chest. At awkward times, Momiji is the recipient of panty shots and jokes about the type of panties she wears. Her relationship with Kusanagi takes a turn for the better during the shielded town incident, where she finally confesses her love for him, and he in turn tells her to wait for him. Voiced by: Megumi Hayashibara (Japanese); Amanda Winn-Lee (English), Monica Rial (English, OVA)
• Mamoru Kusanagi (草薙 護, Kusanagi Mamoru): He was given seven mitama with the expressed mission that when he was older, he would protect the Kushinada from harm. He was very close to Kaede, Momiji's twin sister, before her sacrifice in the tunnels of Tokyo. After Kaede's demise he goes to Momiji to kill her, in order to be free of the Aragami. He comes around, however, in the second episode, and from then on makes it his sole purpose to keep Momiji from harm. He eventually falls in love with her. Kusanagi often pokes fun at Momiji's choice of panties just to anger her. Kusanagi gains his 8th mitama from Momiji when he rescues her from danger in the last few episodes, which gives him the power to fight Murakumo on an even level. Voiced by: Kazuhiko Inoue (Japanese); Jaxon Lee (English), Matt Kelley (English, OVA)
• Daitetsu Kunikida (国木田 大哲, Kunikida Daitetsu): Daitetsu, or Mr. Kunikida, is the Chief Director of the TAC. When Kaede and Momiji were born, Mr. Kunikida raised Kaede like his own daughter, but he exploited her ability to track down and kill the Aragami. When Kaede sacrificed herself, he felt heartbroken. With Momiji in the TAC, Mr. Kunikida decides not to exploit her abilities like he did with Kaede and instead treats her like a normal girl. He usually drives a Citroën XM. Voiced by: Akio Ōtsuka (Japanese); Rob Mungle (English)
• Azusa Matsudaira (松平 梓, Matsudaira Azusa): Azusa is the science officer and experimental biologist in the TAC. Azusa is rarely on the field due to her research and development background. She constructs biological weapons for the TAC to use against the Aragami. She is a divorced mother of one. Voiced by: Yoshiko Sakakibara (Japanese); Sharon Shawnessey (English)
• Ryouko Takeuchi (竹内 涼子, Takeuchi Ryōko): A former member of Tokyo Metropolitan Police, Ryoko uses her police instincts to help the TAC. Ryoko uses her standard police issue weapons in conjunction with weapons modified to be used against the Aragami. She is in love with Kunikida. Voiced by: Ai Orikasa (Japanese); Marcy Rae (English)
• Koume Sawaguchi (沢口 小梅, Sawaguchi Kōme): Koume wears a pink jumpsuit, but never acts feminine. She is loud, brash and aggressive due to her stint in the Japan Self-Defense Forces. She was discharged by the SDF and transferred to the TAC as a result of insubordination. Her philosophy is based on the "bigger gun" theory and she uses her military mind and muscle to destroy the Aragami. She has a soft spot for puppies, enjoys playing matchmaker to Momiji and Kusanagi, and at the end of the series, falls in love with co-worker Yaegashi. Voiced by: Kotono Mitsuishi (Japanese); Tiffany Grant (English)
• Yoshiki Yaegashi (八重樫 良樹, Yaegashi Yoshiki): The stereotypical computer nerd, Yaegashi does computer analogy for the TAC. On off days, he enjoys hentai games on his computer. He also has a program that pinpoints the Aragami's weak points and attacks, but it doubles as a program to predict what animal would appear on Momiji's panties. He has a love/hate relationship with Koume through most of the series. He becomes engaged to her in the OVA. Voiced by: Yūji Ueda (Japanese); Kurt Stoll (English)
• Sakura Yamazaki (山咲 桜, Yamazaki Sakura): Sakura spent most of her life training in the United States. She works as a private occult investigator, using Shinto magic and magic seals to stop the Aragami. She often flirts with Kusanagi, as she finds him both attractive and a suitable partner for her work, and does not consider Momiji a serious competitor for his heart. Though she is featured in the title sequence alongside the main cast, she does not debut until episode 8 and appears only sporadically throughout the series. Voiced by: Sakiko Tamagawa (Japanese); Allison Keith (English)
• Kaede Kunikida (国木田 楓, Kunikida Kaede): Kaede is the twin sister of Momiji and Kunikida's adopted daughter. Her talents were used to detect Aragami for the TAC, but after realizing she was merely a tool and not a person, she sacrificed herself, only to return on the side of the Aragami. Voiced by: Mitsuki Yayoi (Japanese); Amanda Winn Lee (English)
• Susano-Oh (スサノオ, Susanoo): Susano-Oh is an all-powerful god who is the guardian deity of the Aragami. In the legend, Susano-Oh killed the monster Yamata-no-Orochi and married the Princess Kushinada. Kaede and Murakumo awakened him as part of their plan to create a world of nothing but plants. Voiced by: Jun Kitagawa
• Murakumo (ムラクモ): Murakumo was chosen by the Aragami to kill rogue Aragami, those who do not serve the will of Susano-Oh. He has embraced the power of the Aragami and plans on unleashing that power against humanity. Murakumo has eight mitama embedded in his body. Voiced by: Jouji Nakata (Japanese); Aaron Krohn (English)
• Valencia Tachibana (バレンシア・タチバナ, Barenshia Tachibana): Valencia shows up in the OVA. Like Kusanagi, she was implanted with a mitama without turning into a full aragami. Voiced by: Junko Iwao (Japanese); Kira Vincent-Davis (English)

The manga's complete title is Aokushimitama Blue Seed (碧奇魂ブルーシード). Originally serialized by Takeshobo in Comic Ganma between March 1992 and June 1996, its 17 chapters were also collected into two Japanese Tankōbon volumes.

Apart from the opening and ending themes and "Shinshin o Tobikoete" (星を飛び越えて; 'Leaping Over the Stars') (the song sung as a competitive duet by Momiji and Sakura in episode 8), the music for the TV series was composed by Kenji Kawai. Most of the themes were composed to accompany scenes in the first three episodes, though some ended up not being used in the scene they were written for and debuted in later episodes instead.^[5] The music for the later episodes used a combination of these unused themes, some new themes, and repurposed themes from the first three episodes, often with new arrangements that drastically changed the tone of the music.^[5] The TAC's theme, "Otomegokoro ga Moeru Toki" (乙女心が燃えるとき; 'When a Maiden's Heart Burns'), was especially popular with fans of the series.^[6]

"Shinshin o Tobikoete" originated as 'No No Pessimist', the theme song for the never-released Popful Mail OVA. Megumi Hayashibara, the Japanese voice actor for Momiji, wrote new lyrics and retitled the song, recording it for her 1994 album Sphere and then re-recording it as a duet for episode 8 of Blue Seed.^[7] Hayashibara also sang and wrote the lyrics for 'Touch and Go!!', the ending theme of Blue Seed.

Two soundtrack albums were released by King Records on its Star Child label, Blue Seed Ongakuhen Vol.1 (Blue Seed 音楽 Vol. 1) (1994) and Blue Seed Ongakuhen Vol.2 (Blue Seed 音楽 Vol. 2) (1995). In addition, ADV Music released a collection of J-pop songs sung by members of the show's Japanese voice cast under the title Blue Seed.

Opening

• Carnival Babel by Takada Band (Fumihiko Tachiki and Ami Mimatsu) (remade by Megumi Hayashibara as "Carnival Babel 2003 ver." also known as "Carnival Babel Revival")^[8]

Ending

• Touch and Go!! by Megumi Hayashibara
• Life by Megumi Hayashibara (Ep. 26)

A role-playing video game entitled Blue Seed: Kushinadahirokuden (ブルーシード 奇稲田秘録伝, Burūshīdo Kushinada Hirokuden; lit. 'Blue Seed: The Secret Records of Kushinada') was released by Sega for the Sega Saturn on June 23, 1995. It follows an adventure format, and utilizes a card-based battle system. The game's story is not an adaption of either the manga or the TV series, but a set of original episodes set in the same continuity as the TV series. The main cast of the TV series reprised their roles for the battle sequences and introductory cutscene.

The game was one of 12 Sega Saturn games announced when the system was first unveiled at the 1994 Tokyo Toy Show.^[9]

On release, Famicom Tsūshin scored the game a 28 out of 40.^[10]