A mysterious orb envelops the city of Tokyo. All forms of communication are severed, leaving the inhabitants of "Tokyo Jupiter" ignorant to their fate. Along with the United Nations, a special organization known as TERRA is formed: their mission is to liberate Tokyo from the otherworldly MU – those responsible for Tokyo’s capture.

Tokyo citizen Ayato Kamina's life is about to undergo a drastic change. MU agents in dark suits attempt to kidnap both him and his childhood friend Reika, and a sassy TERRA operative brings him face-to-face with the mythical giant robot RahXephon – a force he alone has the ability to control. With everything he has ever known to be true falling to pieces around him, Ayato resolves to fight the MU and protect Reika at any cost!

Story by Yutaka Izubuchi and BONES and Art by Takeaki Momose.