A virtual world in a scab coral (coral-like information life form) created by Eureka. Ten years have passed since the people of the virtual world appeared on this earth with the collapse. As a result of this “great fusion”, human beings in the virtual world call themselves “Green Earth”, and human beings on the old Earth call themselves “Blue Earth”, and various collisions will be repeated under the surface of the water. And Dewey Novak, a high-ranking official of the Green Earth Army, raises up with his colleagues to protect their dignity and finally puts into action a large-scale terrorist program.

来自异次元的种族MU占领了东京，并将城市隐藏在巨大的防护壁之后，他们欺骗在东京生活的人们他们已经成为世界上仅存的人类。在防护壁之外，名为“TERRA”的反MU组织声势渐渐壮大。某日，在同MU激烈交火之时，一位名为神名绫人（下野紘 配音）的平凡少年意外的来到了位于东京湾的地下神殿之中，在这里，绫人见到了巨型机器人“Rahxephon”，并且成为了它的驾驶者。
在神秘女子的紫东遥（久川绫 配音）的带领下，绫人来到了防护壁之外，加入了TERRA，并且在那里遇见了名为如月久远（桑岛法子 配音）的女子。MU组织对TERRA发起了进攻，当TERRA的存亡陷入危机之中时，绫人再一次驾驶着Rahxephon，成为了这个组织的救世主。

Renton, son of scientists, and Eureka, a girl who can't live under the sun, are raised together when very young and become very attached to each other. One day, Eureka is taken away. Powerless at the time, Renton vows to rescue her. He enters the military and is soon is assigned to the Independent Youths Unit 303 of the First Mobile Forces thanks to his exceptional performance alongside his Nirvash, a bio-mechanical armor/control system. Unknown to Renton, lies a plot to extinguish the alien invasion that is currently happening involving not only him, but Eureka too.