In episodes #1, 2, and 20, it is hinted that Reika is not a normal human being. She does not have a reflection unless she needs to, Ayato is able to call her at an unassigned phone number, and she appears to alter Ayato's classmates' memories to make them remember her. She later appears as an aide to Makoto Isshiki, apparently altering TERRA personnels' memories in the same fashion. It is revealed that Reika is actually Ixtli, the soul of the RahXephon, and that her appearance is a manifestation of Ayato's innermost desires. This enables him to connect with and fully use the RahXephon; in artistic terms, she is his muse. Her form is chosen to closely mimic that of a young Haruka Mishima (later Shitou) with whom Ayato had fallen in love. This is to ensure that the performer, or instrumentalist, is more cooperative to Ixtli and more trusting of her than would initially be the case. Ixtli appears to Quon as Reika at first but later takes the guise of Ayato as he has become very important to her.
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.
Reika is the focus of an important and recurring visual leitmotif used throughout the series. She stands on a higher point, with her back facing Ayato, and slowly turns around to smile upon him. This image is also repeated in Ayato's paintings. The origin of the leitmotif is shown in the "Dandelion Girl Coda" at the end of the series.