Since shortly after Pearl Harbor, Johnny had been serving as a common sailor in the U.S. Navy, assigned to the U.S.S. Grover Cleveland, a laundry ship in the south Pacific. Shortly after his mysterious disappearance (known for his clumsiness, he was presumed to have fallen overboard and drowned), the U.S. fleet began to be attacked from well behind the front lines by superpowered Badhanesian natives.
Naturally, the JSA was sent to investigate, and they took some of the Mystery Men along. The heroes were assigned to the flagship of the fleet, none other than the U.S.S. Enterprise. Naturally, the captain of the Enterprise acted quite a bit like this guy:
Much parody ensued: a drunken grumpy southern chief-medical officer, a chief engineer with a scottish accent, and arch-enemy of the ship in the form of a Japanese captain named Kanamoto (or "Kaaaaaan-amoto"), and of course the good captain seducing badhanesian women left and right in complete breach of protocol. A pair of security crewmen with red shirts came on the expedition and met untimely ends. A good time was had by all (except for the red-shirts, of course).
In the end it turned out Johnny Thunder had been kidnapped by an evil Badhanesian witch doctor who was using the Thunderbolt's power to try to take over the world. With Johnny freed and the witch doctor meeting his untimely demise in a volcano, all was well. Johnny was reassigned (much to the relief of the U.S.S. Grover Cleveland's crew) as a U.S. occupation governor for Badhanesia for the duration of the war, to teach the natives the virtues of American-style democracy.
As for the U.S.S. Enterprise and their crew, they would go on to explore new regions of the Pacific and blow them to bits, in the process becoming the U.S. Navy ship with the most commendations in American military history, and ending up getting a famous spaceship named after it.
Currently Smoking: Blatter Diplomat + C&D's Crowley's Best