Maya is the alleged mother of Ayato. In reality though, she's the aunt and adoptive mother of Ayato, but I'll get to that later. Maya Kamina is a very complicated character, especially because much of her past is shrowded in mystery, we only get little hints and tidbits of information here and there throughout the show; only by rewatching the show can you pick up on most of these. Maya is one of the most important characters in RahXephon and deservedly so.
Her original name is Maya Al Padis. Maya is one of the twin girls that Dr. Rikudoh and his assistant Watari Shirow found in the Shrine of Time in 1989. When she came out of the shrine she had no memory of her past life as a Mulian, and in essence was just a regular human girl. She was adopted by Rikudoh and most likely lead a normal life for a while. When she was adopted she acquired the name Maya Rikudoh. Maya was also an instrumentalist and a candidate pilot for the RahXephon. In fact, the original plan of the Mu was so that the two girls pilot the two Xephons and use the RahXephon for Mulian purposes only.
However, Maya awakens too early to be a perfect instrumentalist and instead decides to help the Bahbem foundation create the perfect human instrumentalist as the Xephon requires. It was most likely during these years that Maya met Shirow and the two started dating and eventually got married, making Maya's name change to Maya Kamina. (Shirow's original name was Shirow Kamina, not Shirow Watari, more on this later).
In 1998 the twins Ayato and Itsuki were born, they were brought together by Quon's and Shirow's DNA --in essence, Ayato is Maya's nephew. The two boys were to be raised on different environments and hope that one of them will fulfill their duty as the perfect instrumentalist. Itsuki was taken under the care of Bahbem's household along with Helena and Makoto, and Ayato was entrusted to Maya and Shirow Kamina to be raised in a more normal home. Nature versus Nurture? Probably so.
This would then create an opportunity for the tuning of the world to favor the Mulians. If Maya could somehow raise Ayato and teach him to love her and only her, then the tuning of the world would favor Maya's wishes and in turn also come to favor the Mulians. Because of her goal with Ayato, she often saw Ayato as nothing but a tool to engineer her goal. But even so, Maya raised Ayato as a normal boy and it becomes quite evident that she grew to love him as any mother would love her son.
During the time Ayato was being raised he went on to visit Shirow who was still working in the ruins, there he met Haruka Mishima and the two quickly became friends and eventually lovers. This could prove disastrous to Maya's plans for Ayato as her instrumentalist as it would shift his love to someone else other than her, making Ayato's tuning of the world favor his happiness with Haruka instead of his happiness with Maya --she wanted Ayato to favor the Mulians. If she were to force Ayato from not seeing the girl he loves (Haruka) then it can only make Ayato hate her, which is what Maya is trying to prevent. But how can Maya prevent Ayato from loving Haruka without making it seem forceful?
When the Mulian city of Hiranipra suddenly appeared in the sky, Maya thought she could kill two birds with one stone by creating a protective barrier around Tokyo. It would defend the floating city from attackers and also alienate Ayato from the outside world, including Haruka. This barrier is later codenamed "Tokyo Jupiter" because its surface resembles that of the planet of Jupiter. By doing this, Ayato can still lead a normal life but under Maya's total control. Very convenient for Ayato as he would've been raised as both an instrumentalist but with the normal life Ayato always wanted. Maya went to the extent of even erasing Ayato's mind from everything he knew outside of Tokyo, including his memory of Haruka (all of which one couldn't be erased --Mishima) and convincing the rest of Tokyo that the barrier she created is the only thing that protects them from outside attackers, such as the Mu --of course Tokyo isn't aware of the Mulians within them. This way life continues on normally inside of Tokyo.
While Maya was busy creating the Tokyo Jupiter barrier and conditioning Ayato's memory, Shirow was away with Rikudoh still studying the Neirya ruins. With everything that has happened, Maya and her crew are labeled traitors to humanity for the seclusion of Tokyo from the rest of the world and for working with the Mulians --on top of being a Mulian herself. We know this from when Futagami shows Ayato a picture of her mother as the leader of the Mu along with Kuki, Miwa, and a few others. To avoid serious reprucisions Shirow Kamina changes his name to Shirow Watari. Maya and Ayato however, still keep the Kamina last name.
After all the precautions Maya took to ensure Ayato's future, it all comes crubling down when Haruka succeeds in getting Ayato and the RahXephon outside of Tokyo Jupiter. Maya later acts by sending her Dolems to recover both Ayato and the RahXephon as well as her twin sister Quon. Unfortunately Ayato kills off every single one of them with the RahXephon. Later in the series, Maya's motherly feelings for Ayato win over her Mulian objectives and even helps Haruka find Ayato so that he could obtain his happiness.
Despite all her plans getting ruined, Maya always kept her cool. The only exception was when one of her subordinates talked back to her. Maya's definitely one of my favorite characters in the series.