The series received critical acclaim and was subsequently translated, released on the DVD and aired in several other countries, including the United States.

The series was also spun into novels, an extra OVA episode, an audio drama, a video game, illustration books and an altered manga adaptation by Takeaki Momose.

Izubuchi says the name RahXephon lacked a real meaning, but that he now explains it as composed of Rah as the origin of Ra according to Churchward, X as the unknown variable or X factor, and -ephon as a suffix for instrument from "-phone".

The series makes clear that all of the humans within Tokyo Jupiter are subject to the same kind of mental control, thinking that they are all that's left of mankind after a devastating war.

Ixtli, RahXephon's soul, also adopts Haruka's appearance and family name (Mishima) to guide Ayato, but takes a different given name—Reika.

The story begins as Tokyo comes under attack by invading aircraft while a mysterious woman, later revealed to be Haruka, stalks Ayato.

Because of this and her now having a different last name, Ayato does not recognize Haruka and also initially does not fully trust her, but he gradually re-discovers his love for her as the series progresses, and he learns of everything that has happened.

At the end of the series, Ayato's RahXephon merges with Quon's, allowing him to modify the past by "re-tuning the world" to make it so that he and Haruka are never separated.

Haruka Shitow, an agent of the defense research agency TERRA (acronym for Tereno Empireo Rapidmova Reakcii Armeo, broken Esperanto for Earth Empire Rapid Response Army), brings Ayato and the RahXephon to their headquarters.

Quon Kisaragi, a mysterious girl living with chief researcher Itsuki, seems to share some of Ayato's artistic talent.

Dolems are made of clay, like golems, but are animated by a quasi-mystical force connected to music, as most of the controlling Mulians appear to be singing.

[8] Hashimoto's compositions range from piano sonatas and acoustic chamber music to experimental jazz, hard rock, and ambience that crosses the border into sound design.

The rest of the movie consists mainly of abridged scenes from the original series, sometimes with characters replaced or with different motivations and dialogue.

With the manga Momose got the opportunity to re-design the characters into his own style and make changes in characterization and story,[11] as well as adding "fan service".

The distributor claimed that RahXephon was met with "strong sales and extraordinary critical response in the U.S."[22] The series was generally well received by English-language reviewers.

Protoculture Addicts editor Claude J. Pelletier chose RahXephon as one of the top 3 anime television series of 2002,[23] and Miyako Matsuda agreed, noting mystery, technology, and romance.

[24] Christian Nutt of Anime Jump offered a contrary opinion: "RahXephon's characters fell flat and the grind of its scenario didn't inspire much curiosity, despite some initially awesome ideas".

[30] RahXephon's "brief but not unwelcome" comic moments went over well with Huxley,[31] and he found the romance "a million miles away from the cheery antics of Love Hina or Ranma ½" and "for the most part thoroughly believable".

[30] Chris Beveridge of Anime on DVD found the final episodes beautiful both in visual style and story, "with the raw emotions coming out of it, in both languages".

[30] Anime News Network columnist Zac Bertschy called RahXephon a "paragon of responsible storytelling (...) No loose strings are left; we see the conclusion of every character’s storyline."

Christian Nutt was not excited about the TV series but found the movie to be better: Despite "too much cutting and chopping", he wrote that "the creators have done the best they can with the material."

"[34] Carlo Santos, writing for Anime News Network, recommended the movie both as an "endcap to a remarkable series" and as a sample for those yet to watch it.

Mitchell Hattaway of DVD Verdict "got lost about ten minutes in", considered the movie a waste of money for anybody but RahXephon completists and wrote that "Bones Animation Studio is guilty of contempt for its audience.

[37] Eduardo M. Chavez of Anime on DVD was not impressed by the first volume of the manga, especially when compared to the TV series; he rated it "C minus", though he said it could have worked as a "parody dōjinshi".

[40] The situation was somewhat improved in the second volume, but reviewers did not recommend the novelization as an alternative to the animated versions — only as a source for learning more about the characters and their internal motivations.

[26][43] John Huxley noted an episode with "soul searching" sequences reminiscent of Neon Genesis Evangelion with a "hint of Twin Peaks".

"[43] Christian Nutt of Anime Jump had seen the entire show when he wrote that "One of my least favorite aspects of RahXephon is its aping of Evangelion".

In contrast, Neon Genesis Evangelion's director stated that he did not know how the show would end,[45] and production was influenced by the reactions that TV executives and viewers had to previous episodes.

I think that in its effort to be purely artistic entertainment, RahXephon knowingly pays homage to both Megazone 23 and Evangelion in the same way Evangelion re-uses the concept of a boy piloting his father's giant robot that was used 20 years before in Mobile Suit Gundam, which itself borrowed the idea from even older shows like Tetsujin 28 and Mazinger.John Huxley found "several similarities" with Neon Genesis Evangelion, but wrote that there were "many, more significant differences",[48] and concluded that RahXephon "deserves to be recognised outside of its comparisons to a certain Hideaki Anno animation.

Anno and Izubuchi, the chief directors of each show, both designed mecha appearing in Mobile Suit Gundam: Char's Counterattack (1988) and they worked together on the Cutie Honey (2004) live action movie.