The story is set in the early 21st century, in which a covert evil organization, Dokuga, led by lord NeoNeros, holds near total political, economic, and military control of the world. Dokuga agents try to forcibly recruit a brilliant physicist, Professor Sanada, who sets off a suicide bomb rather than let Dokuga acquire his secret research. His son Kenta becomes Dokuga's next target, but is saved by his father’s colleague and taken on board a teleporting fortress, Good Thunder. Teleportation is enabled by a mysterious form of energy, called Beamler, which was discovered by Sanada. The same energy also powers a giant battle robot, GoShogun, which is operated by three pilots. The crew of Good Thunder travels the world, repeatedly fighting off NeoNeros's forces with GoShogun and often hampering Dokuga's influence on the local level, whether by destroying their bases and businesses, assisting popular rebellions, or by averting environmental disasters.