Ayato is a student and artist who lives with his mother, Maya Kamina in Tokyo. Most of his artwork shown in the series consists of drawings or paintings of a girl on a cliff looking towards the sea. He has birthmark-like symbols on his belly that resembles runes, which are revealed to be a sign of his being a potential instrumentalist for the mysterious giant godly being called the RahXephon.

After being taken from Tokyo by Haruka and the RahXephon, Ayato moves in with Shougo Rikudo, Haruka's uncle on Nirai Kanai. At first, this arrangement does not sit well with Ayato, as Haruka and her younger sister Megumi live in Rikudo's annex, but they slowly adapt to each others' presences. As a stranger from Tokyo Jupiter, Ayato struggles to find his place and acceptance in the outside world. Although he pilots the RahXephon in defending Nirai Kanai, he questions his abilities and self-worth. He also struggles with trying to piece together and understand his relationship with Haruka, handling the feisty Megumi, and interacting with the other TERRA personnel, who regard him with a broad spectrum of reactions, from acceptance and friendship to cool scientific interest to distrust and even contempt.