Ayato is the main character of RahXephon. He's the pilot of the RahXephon, the one destined to tune the world, and the one who stole Haruka's heart. Being a half Mulian and a half Human, he is often confused as to which group he belongs to, and as such, has a deep inner struggle for what should he be fighting for, and who should he be protecting. He eventually decides to protect his friends and his loved ones, no matter what color of blood.
While noble with his intentions, Ayato usually finds himself doing things he didn't want to do, and really bad things he wasn't even aware of. By deciding to protect his friends from the giant Dolems, he's also killed them in ignorance. Since Mulians are directly connected to Dolems, by killing the Dolem, Ayato also kills the Mulian in control of that Dolem. Of course, not knowing this, he ignorantly killed Asahina as well as Mamoru, his two best friends from Tokyo Jupiter. Of course being heart broke by this, he's usually discouraged to keep piloting the RahXephon.
What Ayato cares the most about is knowing the truth, and also being around people he trusts. When he doesn't get this, he usually tends to freak out, and if the case is dramatic (like at the beginning of the series, or when he sees his mother bleeding blue blood), he'll even scream in fear. One of the bigger issues Ayato tries to address is his own identity. At first he thought he was just a normal person, but when he's informed that he's also a Mulian he suffers a serious identity crisis and even runs away from Terra to Tokyo Jupiter to find more about his true identity. When he encouters his adoptive mother Maya, she reveals to him the truth and Ayato of course freaks out when he finally realizes who his mother really is. Coping with his identity is an important issue in the story of RahXephon and one that is finished quite nicely with the tuning.
Ayato is also Haruka's love interest. And vice versa, Ayato fell in love twice with Haruka: once in high school and again after Tokyo Jupiter. The two were very close during their teenage years but later got separated thanks in large part to Maya. Maya went as far as erasing Haruka from Ayato's memory since it would interfere for the plans she had for him. Since Tokyo Jupiter's time elapses differently from the outside world, he aged much slower than Haruka, and as a consequence Haruka became 12 years older than Ayato by the time they met again. But even with such a big age gap, the two found themselves falling for each other again, and this time, the love is much stronger than before. Haruka and Ayato's romance is one of the central themes of the story and quite literally the fate of the world depends on their love.
After the tuning, Ayato became an Assistant Professor, is married to Haruka and has Quon as his first born. He still loves to paint as a hobby as it is clearly evident by his golden RahXephon paint as well as the painting he and Itsuki shared in mind.
An interesting note to point out is that Ayato's name has a meaning. "Ayato" means one who manipulates, but it also means "one who renders something beautifully." This is particularly interesting when his last name, "Kamina", means "of the gods."