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Have you ever wondered if Lex Luthor knows Superman’s secret identity? He would have to, right? You would have thought that a genius obsessed with someone so much to the point of testing ever possible negative scenario would have discovered Superman alter ego. The answer is yes, Lex finds out that Superman is Clark Kent. But it only took 71 years.
Lex Luthor first appeared in Action Comics 23 in 1940. Almost three quarters of a century later in Action Comics 900 from 2011, the Superman alter ego was finally discovered by him as a result of probing his mind while attempting to cause him emotional pain.
In the main story of the comic, all of the super people (Supergirl, Superboy, Steel, etc) are trapped with Doomsday as a sort of decoy while Lex Luthor encounters Superman in a galaxy far, far away. Lex managed to gain the power of a god, and has the choice to either have limitless power and provide joy to everyone everywhere, or to use the power all at once to try and kill Superman.
Naturally, Luthor decides to try and kill Superman.
Trying to rationalize and show him all the pain he has become a part of, Lex shows Superman all of it first hand, even causing him to revisit his death. While this is going on, we see him mourning the death of his father while back home on the farm. That is when Lex Luthor discovers Superman alter ego, never realizing that he was capable of relating to humans.
As you may have imagined, Action Comics 900 is a special extra-large issue, padded with meaningless and wasteful throw-away stories. The last one even appears to be unfinished, as it simply has thumbnail sketches next to paragraphs, presented as a supposed “screenplay”. There is also a four-page story (and I use the word “story” loosely) where Lois Lane invites Superman’s friends over for an informal dinner party. Cute, but completely unnecessary.
The cool thing about Action Comics 900 is that not only do we get a more complete section of story without having to read multiple issues, but there were several variant covers (Affiliate Link) made by the top artists in the industry. These have included David Finch, Adam Hughes and Alex Ross.
Also in this story, all the super people as mentioned earlier fight Doomsday simultaneously. So it becomes really exciting quickly. To make thing easier on yourself, I suggest getting the graphic novel to help you get a more complete picture of the story.