As Lex's "Legion of Doom" expanded some of it's members grew powerful beyond his control, including Mxyzptlk and Jeremy Creek. Other members learned too much and became a liability, like Molly Griggs. Over the years Lex eliminated many of his agents for these reasons.
Those who survived lived as rogues on the edge of society. Some waited in the shadows, biding their time until Lex was at his weakest, when they would again be gods among men. A few would aid the Justice League from time to time.