[Astromancer]

Although I'll do more Rhiannon later, try this idea...

It a very different Supervillain game. First General Zod ( a Kryptonian who hated Superman's Dad) gets two things a stroke of luck and a clue. The second being far deadlier. Zod decides that, if he wants to remake Earth into Krypton, he'll need to go slow and seduce humanity into helping him.

The stroke of luck is basically a Deux Ex Machina that cleans up Zod's terrestrial criminal record. Basically, no one on Earth, including Supes, remembers him. So he can simplely pose as a loney refugee from the stars with technological knowledge to trade. It through introduction of chosen technologies Zod means to disrupt Earth and get folks to go along with his ideas to solve the problems of change. A fairly simple and effective sceme. Since Zod had Kyptonian longevity treatments, which baby Superman didn't have ( the longevity treatments are very bad for babies and other immature Krypttonians) Zod knows he has millenia to work his sceams.

But even if the Justice League can't focus on Zod, they've got other problems, other folks can see Zod's actions as a threat. Zod is bringing useful technologies suited to solve Earth's greatest problems. He's even used the fact that he's from Krypton as an advertisement for the quality of his tech. This immediately would catch the attention of Lex Luther, who sees Superman as a threat to Earth's development. Veronica Cale, a Wonder Woman foe who sees all supernatural and alien beings as contaminating Earth. The Parliament of Owls, Batman foes, wealthy conspirators seeking godlike authority. Ras-al-Ghul, the head of the League of Assassins, with his own vision of Humanity's future. And Vandal Savage, the immortal foe of the Flash and Hawkman, who seeks to be godking of Earth. All would quickly see Zod as a threat.

The idea would be the PCs are high-level agents of one or more of the above mentioned supervillains. Your goal would be to either spy on Zod ( a sly old paranoid with senses like Superman) or to stop his technological innovations. Between the foe and your bosses, life could get scary.