At first, this arrangement does not sit well with Ayato, as Haruka and her younger sister Megumi live in Rikudo's annex, but they slowly adapt to each other's presences.
He also struggles with trying to piece together and understand his relationship with Haruka, handling the feisty Megumi, and interacting with the other TERRA personnel, who regard him with a broad spectrum of reactions, from acceptance and friendship to cool scientific interest to distrust and even contempt.
Conceived with the help of Ernst von Bähbem and raised by Maya as an instrumentalist — someone who can successfully use the RahXephon to re-tune the world.
A 29-year-old officer within the TERRA organization, Haruka Shitou is partially responsible for aiding Ayato in leaving Tokyo Jupiter.
Her form is chosen to closely mimic that of a young Haruka Mishima (later Shitou) with whom Ayato had fallen in love.
Despite disappearing often, Ixtli/Reika Mishima is quite caring of Ayato, and will go the extra mile to see that he fully matures into his role as 'Ollin' and punishes those who would ruin her goal of a successful 'tuning'.
Although Ayato initially rejects Reika after he learns the truth about her and what she is, he later chooses to accept her and become one with the RahXephon, thus enabling him to re-tune the world.
Quon Kisaragi is a mysterious young girl who speaks the first words of the TV series and is shown meeting Ayato in episode 4.
She is also one of the few people who never treats Ayato as a curiosity or an annoyance, and she seems to have an understanding of his situation and what his eventual role is, calling him "Ollin" ("motion" in Nahua).
She and Ayato are both shown undergoing examinations, and while outside of her home she wears a vest-like device called a Life Module.
In the designs created by Akihiro Yamada and adapted by Hiroki Kanno, Quon is shown wearing a short dress with long sleeves, the Life Module, high heeled shoes, a thigh strap (worn like a garter), a beret, and a parasol, leading to a stereotypical "French" look.
In some illustrations, like Yamada's DVD 2 cover design (used in France and Japan, but not in the initial U.S. and UK release), Quon wears a frilly lace-trimmed dress and stockings, which with the parasol complete a "Gothic Lolita" look.
In Ouran High School Host Club, another anime series by Bones, the "French" otaku Renge is shown cosplaying as Quon on one occasion.
The Mu refer to the robot as "Xephon", adding the honorific of "Rah" near the end of the series when Ayato is ready to tune the world.
It is revealed, through flashbacks in the series as well as in the movie prologue, that Hiroko was in love with Ayato while they were in their early teens, before Tokyo Jupiter was created, and that her feelings have not subsided even though she is dating Mamoru.
Here, Asahina escapes from Tokyo Jupiter with refugees and arrives in Nirai Kanai where she projects three Dolem and holds Reika hostage, forcing Ayato to kill her.
At the end of the series, Miwa briefly expresses doubt over the Mu agenda before finally becoming bound to the Dolem Allegretto.
Kunugi was an officer of the Japan Self-Defense Forces, under the command of Kuki Masayoshi, who ordered him to perform a nuclear strike on the Mu.
It is also strongly hinted that Kim becomes pregnant by Souchi, as she appears to be suffering from morning sickness in two scenes near the end of the series.
This leads to a small running gag in the series: Whenever she is particularly upset about Itsuki, the windscreen wiper on her car is shown to make an interval swipe on its own.
She is freed by Ayato in the RahXephon, and later enters into a relationship with Makoto Isshiki and supplies him with information, thus unwittingly keeping the Bähbem Foundation abreast of Quon's status.
Elvy Hadhiyat is an ace pilot for TERRA, and participated in the operation to extract Ayato from Tokyo Jupiter in episode 1.
Elvy parallels Lydia Litvyak, a World War II female fighter ace nicknamed the "White Rose of Stalingrad" and the namesake of the ship in the series.
She is later killed in battle against the Mu when Ayato unites with the RahXephon and sings a 'song' which produces a wave of destruction that destroys her aircraft, surrounding Dolems and various TERRA sea vessels.
Makoto Isshiki, called "The White Snake" because of his albinism and personality, is sent by the Earth Federation to observe at TERRA.
Isshiki has Kunugi removed from his command position, and leads Operation Downfall to destroy the Tokyo Jupiter barrier.
Shirou Watari is the director of TERRA, and spends a lot of time on the road facing the press, lobbying for the organization, and coordinating with the Bähbem Foundation.
Masaru Gomi and Youhei Yomoda work with Haruka, Megumi and Kim in TERRA's operations room.
Rikudo has an equally prominent position in the movie as in the series, and he takes on a greater importance in telling the story.
Johji Futagami is a Columbo-like reporter from Amato News who is given exclusive press access to TERRA, making his way around the island of Nirai Kanai asking questions of both principal characters and other local residents.