Kamina Ayato lives an ordinary life. He goes to school. He lives with his mother. He has schoolmates. But all of that changes one day when massive machines, known as the Dolem, attack the city of Tokyo with their destructive vocal powers. Caught up in the chaos, Ayato meets a mysterious girl named Mishima Reika. She leads him to the sanctuary, resting place of the RahXephon, a giant humanoid being with powers to counter those of the Dolem. Upon its awakening, Ayato finds himself synchronising with the machine and it takes him to the world beyond Tokyo. It seems that Tokyo, more precisely called Tokyo Jupiter, has been cut off from the rest of the world. Those living within the boundaries of Tokyo Jupiter believe that the rest of the world has been decimated, when in fact they live in a world controlled by the Mu. Now, facing the truth, Ayato must come to terms with his new reality, for he is a central element in the fate of mankind.