The mundane existence of high school student Ayato Kamina is upended when Tokyo is suddenly attacked by futuristic fighter jets. In the midst of the turmoil, he meets a woman named Haruka Shitow, who states she belongs to a government agency known as TERRA. She discloses that he has been residing within a time bubble dubbed "Tokyo Jupiter," established by the Mulians—humanoids from another dimension—in an effort to isolate and seize control of Tokyo. TERRA has been attempting to breach the barrier encircling the city ever since. Overwhelmed by this revelation, Ayato panics and runs away. He encounters his classmate Reika Mishima, who guides him to a location known as "The Shrine of Xephon," where a massive egg rests. She begins to sing, and an unknown power awakens inside Ayato, linking him to an entity called RahXephon that bursts from the egg. Soon after, Haruka locates him once more and attempts to persuade him to join her campaign against the Mulians. Caught between the Mulians and TERRA, Ayato starts to question his purpose, navigating through altered memories and ultimately his own identity in this chaotic new world.