Ayato Kamina was separated from the girl he loved, Haruka Mishima, when an event occurred that was thought to have killed everyone outside of Tokyo. But one day three years later, invaders suddenly attacked the city. It was then that he meets an agent of TERRA, Haruka Shitow, who tells him that she will give him the truth about the world. It is the beginning of a series of strange events, which involve him activating a giant mecha, the RahXephon and finding out that many people, including his own mother, has blue blood, and that he was actually living in a self-encased dimension where time moves slower than that of the outside world. (Source: ANN)

The ordinary life of high school student Ayato Kamina is turned upside down when Tokyo is suddenly invaded by futuristic fighter jets. Amidst the chaos, he encounters a woman called Haruka Shitow who claims to be from a government organization called TERRA. She reveals that he has been living in a time bubble named "Tokyo Jupiter" that was put in place by the Mulians—humanoids from another dimension—in an attempt to isolate and take over Tokyo. TERRA has been trying to break through the barrier surrounding the city ever since. Unable to process the revelation, Ayato panics and flees. He runs into his classmate Reika Mishima who leads him to a place called "The Shrine of Xephon" where a large egg slumbers. She starts to sing and an unknown power awakens within Ayato, connecting him to a being called RahXephon that breaks out of the egg. Shortly after, Haruka finds him again and tries to make him join her cause of fighting against the Mulians. Caught between the crosshairs of the Mulians and TERRA, Ayato begins to question his purpose, navigating altered memories and ultimately his very identity in this chaotic new world. [Written by MAL Rewrite]