The Protagonist of the series. An artistic youth, he finds himself drawn into a chain of events beyond his capacity to understand and through the people around him he has to find his place in the world.
- A God Am I: Happens once he's merged with the RahXephon. He does a good job of fixing things once he does, though.
- Age-Appropriate Angst: Of the existential variety. He never descends beyond what's understandable, either.
- Chick Magnet: To the point where some people consider this show a Harem Series.
- Dangerous Sixteenth Birthday: He celebrates his 17th birthday by the time the story begins.
- Determinator: No matter how much he has suffered or how much he is attacked by the Mu, he refuses to lose.
- Falling into the Cockpit: Subverted: Ayato has been prepared for piloting the RahXephon his entire life, he just doesn't know it until midway through the series.
- I Know Mortal Kombat: Inverted: Because he pilots the RahXephon, he's none too shabby at aerial dogfight arcade games. He's no match for Ace Pilot Elvy, though.
- Likes Older Women: Averted. One of the first things he says to Haruka is that he doesn't like older women. Luckily for her, he falls in love with her just as much as he did with the teenage one.
- Lotus-Eater Machine: Vivance the Dolem traps him in one of these. He breaks out because of Reika and beats the hell out of Vivance with RahXephon's help.
- Male Gaze: As he's introduced to the cast, the camera has a tendency to fixate on the particular features of the ladies.
- Technician vs. Performer: Ayato's (artistic) ability to pilot the RahXephon is contrasted by Itsuki's failed (scientific) attempts
- Time Travel: Not literal, but he feels like this after being brought out of Tokyo Jupiter, comparing himself to Urashima Taro (Japanese Rip Van Winkle and main character of the first documented story about time travel).
- Tomato in the Mirror
- What Measure Is a Non-Human?: When the Mu Phase in his blood activates, the people around him begin to have doubts about how trustworthy he really is. He proceeds to prove them all wrong by being such a decent guy.
- You Are Not Alone: For the finale
- All Love Is Unrequited: Or rather erased due to Mulian mental conditioning.
- Christmas Cake: 29 years old. Downplayed in that her age isn't really brought up much and Megumi is even a little jealous of her managing to be fairly girly despite her age (like maintaining a crush on the same guy since she was a teenager).
- Femme Fatale: Subverted. Her introduction paints her as a shifty and potentially dangerous person, future episodes reveal her to be nothing but sweetness and fun.
- May–December Romance: Played straight until the very end where it's subverted because Ayato's re-tuning resulted in him growing to be the same age as Haruka.
- Mysterious Protector: In a roundabout way throughout the entire series.
- Spanner in the Works: To Maya's plans.
Voiced by: Maaya Sakamoto, Mandy Clark (EN)An ethereal girl in a yellow dress who Ayato seems to recognize from somewhere. She definitely knows more than she lets on and is connected to the secrets of the RahXephon.
- Cryptic Conversation: Which also fully explain the plot.
- Deus ex Machina: A completely justified one.
- Does This Remind You of Anything?: Her attempt to truly awaken the RahXephon in episode 23 is rather like an Immodest Orgasm.
- Mind Control: Will invoke this on people in order to get them to guide Ayato towards his destiny.
- Voluntary Shapeshifting / Empathic Shapeshifter: As the soul of the RahXephon she takes the form of the person most important to her pilots. Since the RahXephon was split in two she had to guide two pilots. For Ayato this was a younger Haruka. For Quon it was Ayato.
- Cryptic Conversation: Pretty much whenever she says anything.
- Demoted to Extra: She sleeps through almost the entire movie.
- Genius Ditz: More like Genius Cloudcuckoolander. She learns shogi (Japanese chess) from Rikudoh. The next time the camera focuses on them (in the same episode), Rikudoh is noticeably having a hard time in the game.
- Luke, I Am Your Father: It turns out that Quon is in fact the biological mother of Ayato and Itsuki, and is Maya's older twin sister.
- Impossible Hair Color: Dark pink, long and usually in a braid.
- Older Than She Looks: Quon is Maya's older twin sister, but has only aged since leaving stasis right before the formation of Tokyo Jupiter.
- Shameless Fanservice Girl: "To be perfectly honest, I'd like to take off everything...but if I came here to get my haircut naked I'd probably get scolded, don't you think?"
- Verbal Tic: "Ra ra?" which she uses when she's surprised or as an equivalent to what most people would respond with a "what."
- You Gotta Have Blue Hair: Quon has pink hair.
Voiced by: Mitsuru Miyamoto (JP), Jay Hickman (EN)A scientist of TERRA and brother of Quon.
- Big Brother Instinct: Ironic considering he's actually Quon's son and Ayato is his older brother.
- Brother-Sister Incest: Nothing explicitly overt, but his affection for Quon is a tad bit obsessive.
- Cain and Abel: He's a good guy despite an upbringing under Bähbem. His dynamic with Ayato is quite interesting, though not as vicious as other examples of this trope.
- Defrosting Ice King: He's quite aloof in the first part of the series. Once his motivations are fleshed out, however, he becomes more nicer.
- Luke, I Am Your Father: Itsuki reveals himself as he is Ayato's twin brother.
- Replacement Goldfish: To Haruka, in a sense. It's heavily implied that she once had a relationship with Itsuki because he looked like Ayato.
- Berserk Button: Don't call him "D" or he will get mad.
- The Casanova: He used his sexual conquests to gather information about goings on in TERRA and to gratify his own ego, with no concern for his partner's well-being.
- Character Death: He dies when he gets shot by Laila Costa.
- Cloning Blues: Eventually leading to his emotional meltdown.
- Deadpan Snarker: He'd be very funny, were he not such a condescending bastard
- Evil Albino: He has light skin, light hair and is a villain.
- Meaningful Name: "Isshiki" means "one color." Take a wild guess at which one. Whereas Makoto means either "truth" or "faithful" depending on how it is written. Considering his casanova personality and origin as a clone neither really apply to him. Although knowing his family, this naming was probably intentional.
- Smug Snake: Goddamn, is he ever. Characters in the series even call him "The White Snake". It runs in the family.
- Start of Darkness: He may be a callous prick as an adult, but just try and watch the episode about his childhood and not feel like he badly needs a hug. "And I wonder if that clay doll ever found its parents, in the mud?"
- Tragic Keepsake: He's kept a piece of the clay from the Dolem from his childhood that got stuck with a clump of his hair
- The Unfavourite: Especially harsh when your earliest memories are fellow clones suggesting that a short life expectancy for you might be "a small mercy".
- Villainous Breakdown: After he brings down Tokyo Jupiter and ends up inadvertently assisting the Mulian invasion plans.
- "Well Done, Son!" Guy: He and to make his father proud, but it ends up contributing to the aforementioned breakdown.
- With Friends Like These...: With Itsuki. The scientist is Isshiki's oldest and closest friend, and Isshiki still treats him like shit.
- Yaoi Guys: There are hints in the early part of the series that he and Itsuki had been more than just friends when were young boys.
Voiced by: Atsuko Tanaka (JP), Kelly Manison (EN)A scientist at TERRA. Works under Itsuki, and harbors some feelings for him.
- Character Death: She commits suicide when she kills Itsuki and realizes the truth from Bähbem.
- Driven to Suicide: After accidentally killing Itsuki and being revealed to be a Tomato in the Mirror.
- Running Gag: Her windshield wipers work on their own when she's in her car and upset.
- Tomato in the Mirror: Bähbem gave her false memories.
- Took a Level in Jerkass: Becomes more and more angry and bitchy as the series goes on.
- Irony: His name means "to protect." After he's revealed to be a Jerkass, he does nothing that supports his name. In contrast, one of the most uttered lines from Ayato is that "he wants to protect" something.
- Jerkass: He's quite a jerk to Ayato. Things got even worse after he discovered that Ayato had killed Hiroko.
- Manipulative Bastard: He REALLY likes to plays off of Ayato's guilt.
- Victorious Childhood Friend: It's heavily implied in the last episode that he and Hiroko ended up marrying each other.
- Character Death: Ayato beats up a Dolem, but that inadvertently leads to Asahina's death.
- Cruel and Unusual Death: Due to her being linked with a Dolem, which Ayato inflicted what would amount to a No-Holds-Barred Beatdown.
- Dying Declaration of Love: Which she desperately writes in a notepad as Ayato is unknowngly killing her via destroying a Dolem she's linked to. Once she dies, the lights of the nearby buildings spell it out to him.
- Fish out of Water: She becomes like this once Ayato brings her out of Tokyo Jupiter.
- Tsundere: To Mamoru. We never see her 'dere' side shown to him, but she's got all the Tsun-Tsun mannerisms. And you see how she acts around Ayato...
Megumi ShitowJapanese: Ayako Kawasumi
English: Hilary HaagHaruka's younger sister.
- Annoying Younger Sibling: But in a sweet and likable way. While she's still older than most examples, she still fulfills this role quite a bit.
- I Want My Beloved to Be Happy: "Megumi Shitow used to have a bit of a crush on Ayato Kamina! But she doesn't anymore! That's what she's decided!"
- He Is Not My Boyfriend: With Ayato. in the later episodes, this attitude starts to change a bit.
Ernst Von BähbemJapanese: Iemasa Kayumi
English: Ted PfisterThe enigmatic director of the Bähbem Foundation. He harbors a special interest in ancient Mayan civilizations.
- Affably Evil: He is exceedingly well-spoke and polite.
- Big Bad: Not only does he give off this air, but he is behind most of the things that drive the plot.
- Character Death: He meets his end when Futagami finally guns him down.
- Dirty Old Man: He seems to enjoy touching the tattoo on Quon's belly far too much. It's even worse in the movie.
- For Science!: His ultimate motivation behind making the RahXephon.
- Grand Theft Me: His means of living so long.
- Immortality Immorality: When your method of choice involves seizing control of people you've raised since birth, it definitely counts.
- Really 700 Years Old: He is old as millennia itself.
- Smug Snake: Now you see where Isshiki and Helena get it from!
- Wicked Cultured: He knows much about fine art and culture, particularly Nahatual cultures. Given that he lived through most of it, this shouldn't be surprising.
Voiced by: Ichiko Hashimoto (JP), Laura Chapman (EN)She is Ayato's mother (or better said, his aunt), a confident and strong woman who wants only the best for her son. She is the leader of the Mu.
- Creator Cameo: Ichiko Hashimoto, the composers of the series, provides Maya's voice in Japanese.
- Graceful Loser: Apparent when she speaks to Haruka in the last episode.
- My Beloved Smother: Well-intentioned, but so very overwhelming to poor Ayato.
- Parental Neglect: Not intentionally. She provides for Ayato but works a lot and doesn't make time for him. Ayato calls her out on it in a dream sequence.
- Pet the Dog: She accepts Rikudo as her father and appears to him to say goodbye before the Tuning.
- Well-Intentioned Extremist: Maya smothered Ayato as a means of influencing him to create a world favorable to her people at the time of the Tuning.
Voiced by: Kouki Miyata (JP), Mark Laskowski (EN)The second-in-command of TERRA and an all around friendly guy. He's also Kim's boyfriend.
- Character Death: He gets shot down when Ayato and the RahXephon sing a song.
- The Pollyanna: He's definitely the most cheerful person in all of TERRA.
- Reverse Mole: When Isshiki usurps command, Souchi goes out of his way to kiss the bastard's ass to make sure Isshiki fails.
Voiced by: Yuu Sugimoto (JP), Christine M. Auten (EN)Leader of TERRA's airforce and friend of Haruka.
- Ace Pilot: She is a top pilot of TERRA's air force.
- Ambiguously Brown: Averted. It's noted in-story that she's from Indonesia and her nickname, "Bunga Mawar," means "Rose Blossom."
- Character Death: Elvy is shot down when Ayato and the RahXephon sing a song.
- Hard-Drinking Party Girl: She is hilarious when drunk. "You wanna lock on? Dogfight 'til morning, cutey?"
- Vitriolic Best Buds: She and Haruka exchange quite a few riffs, despite being good friends.
Commander Jin KunugiHe buried Mulians under the cherry trees in his garden.
- Character Death: He dies after doing a Heroic Sacrifice.
- Cynicism Catalyst: His harsh, businesslike attitude is apparently due to firing the bomb that killed his daughter.
- Dying Moment of Awesome: He decides to take Kuki down with him in his Heroic Sacrifice.
- Heroic Sacrifice: And an absolutely badass one, at that
- Memetic Badass: Invoked. Legend says he buried Mulians under the cherry trees in his garden, which is why the cherries that blossom from his trees are blue.
- Not So Stoic: The scene where he laughs when Ayato asks about the blue cherry blossoms is absolutely priceless.
- The Stoic: He has a calm demeanor, even as a commander.
- Taking You with Me: He does this to Kuki as part of his Heroic Sacrifice.
- A Father to His Men: He buys them all Chrismas presents to make up for leaving them with a boatload of work before the holidays.
- Eyepatch of Power: A unique one - it seems he has perfectly normal right eye, but he wears this anyhow.
- Luke, I Am Your Father: He reveals to Ayato that he is his biological father.
Shogo Rikudohand Maya's adoptive father. Lives on Nirai Kanai island.
Joji Futagami / Takeshi Jumonji
Voiced by: Katsunosuke Hori (JP), Andy Mc Avin (EN)A laid back, bumbling observer sent by Terra to placate the media.
- Catch Phrase: "What's your take on that?"
- Intrepid Reporter: He's a reporter who is given access to the TERRA organization, and he interviews the staff there to get new information.