In JLA #37-38, DC brought back the JSA for the third teamup with the Justice League. Once again, they continued to rotate the characters.
In this story, Johnny Thunder and his Thunderbolt appeared for the first time since the 1940s. Johnny is probably the least famous JSA member. He effectively had a genie (the Thunderbolt) who would appear whenever he spoke the words "Say you". The humor arose because Johnny apparently didn't know those were the magic words, although of course he managed to say them by accident many times. He was a major DC character of the 1940s, appearing in many issues of Flash Comics (including #1) and All-Star (including as a charter member of the JSA in #3), as well as the first three issues of World's Best/World's Finest and World's Fair Comics 1940.
Fate was not very kind to Johnny. In Flash Comics #86, a backup character was introduced named the Black Canary. Six issues later, Thunder was out and the Canary was in; she also fairly quickly eased him from of his role in the Justice Society.
In this story, Johnny does know the words "Say you". He has been invited to a meeting of the JSA once again. However, upon learning that there are Earth-1 counterparts to some of his old mates, he becomes curious as to what his doppelganger is like. It turns out that the Johnny Thunder of Earth-1 is a small-time crook who remembers reading the old Johnny Thunder comics in the 1940s. He kayos Earth-2's Johnny and takes over control of the Thunderbolt.
Realizing that the JLA will be tough to beat, he commands the Thunderbolt to arrange things so that none of the JLA heroes will arise. The Thunderbolt prevents Krypton from exploding, keeps the lightning from breaking through the window of Barry Allen's lab, stops Abin Sur's rocket from crashing, etc. Sadly, Bruce Wayne's parents are not rescued:
Since Johnny has not shown up for the JSA reunion, his old mates are worried. They track him down to Earth-1 where they are stunned to learn that the JLA does not exist. They battle Johnny and his Thunderbolt, but are unable to prevent them from getting away with magic. They discover from interviewing Thunder's henchmen that there are no superheroes on Earth-1 and never have been. So they decide to mimic the JLA themselves, using their powers to fake the Earth-1 heroes' abilities.
They trounce Johnny and the Thunderbolt, but the former soon figures out that it was the JSA members in disguise. In response, he tells the Thunderbolt to arrange for it that five of his cronies become the JLA heroes Batman, Superman, Flash, Green Lantern and Martian Manhunter. Thus his criminal henchmen become supervillians, setting the stage for a battle in the following issue.
In JLA #38, the heroes of Earth-2 battle the villains of Earth-A (since Earth-1 is now an alternate world). But the heroes prove too much for the villains because they are accustomed to using their powers while the villains are still new to the experience. Of course, this makes little sense given that the Thunderbolt had gone back in time to make them super-powered beings:
(Update: Now that I think of it, this is probably why Gardner Fox did not have the Thunderbolt rescue Bruce Wayne's parents, because if they had, what Hawkman would be suggesting here is to allow them to die again.)
Johnny escapes to the moon where he forces the Thunderbolt to create three new villains, but in the end they are defeated, and so it's a battle of the T-Bolt and Dr Fate. But Johnny gets caught up in the fight and is being battered, so he finally wishes that none of this had ever happened.