Set in 2001 A.D., a mysterious orb envelops the city of Tokyo, isolating it from the rest of the world. All forms of communication are severed, leaving the inhabitants of the newly dubbed "Tokyo Jupiter" ignorant to their fate. A clandestine organization known as TERRA is formed, with the mission to liberate Tokyo from the otherworldly Mu -- the group responsible for Tokyo's capture. As a result of the calamity, young Tokyo inhabitant Ayato Kamina's life undergoes a drastic change when Mu agents in dark suits attempt to kidnap both him and his childhood friend Reika. Soon after escaping, a sassy TERRA operative brings him face-to-face with the mythical giant RAHXEPHON robot -- a force he alone has the ability to control. With everything he has ever believed in falling to pieces around him, Ayato must fight the Mu and protect Reika at any cost.