Ayato Kamina was torn from the girl he adored, Haruka Mishima, when a catastrophe unfolded that seemed to have annihilated everyone beyond Tokyo. Three years later, the city was suddenly besieged by invaders. In that moment he encounters a TERRA operative, Haruka Shitow, who promises to reveal the world's hidden truth. This marks the beginning of a chain of bizarre events: he activates the colossal mecha RahXephon, discovers that numerous people—including his own mother—possess blue blood, and learns he has been living in a self‑contained realm where time passes more slowly than outside the sprawling metropolis in a hidden enclave within the city walls where the past and future intertwine.