The mundane existence of Ayato Kamina, a high school student, is thrown into disarray when Tokyo is besieged by fighter jets from the future. Amidst the pandemonium, he encounters Haruka Shitow, a representative of TERRA, a government agency. She reveals that Ayato resides in an enclosed time bubble, "Tokyo Jupiter," which the Mulians, humanoid beings from an alternate dimension, seek to commandeer. TERRA has been endeavoring to penetrate the protective shield around the city but to no avail. Overwhelmed by the revelation, Ayato flees in terror only to encounter his schoolmate, Reika Mishima, who leads him to "The Shrine of Xephon." Here, a colossal egg is dormant. As Reika sings, Ayato plugs into RahXephon, a sentient entity born from the egg. When Haruka reappears, she enlists Ayato's assistance in battling the Mulians. As he is caught up in the conflict between TERRA and the Mulians, Ayato begins to question his raison d'être. He must navigate a murky terrain of fragmented memories and uncertainties concerning his identity in this chaotic new world.