Lois sees Clark outside her window but thinks she's seeing things, and wonders if Luthor might have drugged her. She starts investigating him and turns up some disquieting things about him. Not long after, Clark makes his first appearance as Superman, and Lois realizes that she wasn't hallucinating after all. She confronts him and tells him that she knows who he is, and asks what he was doing outside her window. Clark tells her that he was trying to protect her from Luthor. Lois decides not to reveal that CK=S, because it's more important to take down Luthor than to reveal that her dorky co-worker (who is more attractive than she'll admit) is moonlighting in tights, especially since Clark's powers make it easier to gather information on Luthor. They succeed in taking Luthor down, and by that time Lois returns Clark's affection and won't reveal his secret (even if it would win her a second Pulitzer; she and Clark share the Pulitzer for the story that takes down Luthor).
Luthor never has a chance to clone Lois and interfere in her relationship with Clark, so Lois and Clark get married much sooner and the path of true love goes considerably more smoothly than in canon.
How's that for WAFFy?
"Oh, you can’t help that," said the Cat: "we’re all mad here. I’m mad. You’re mad."
"How do you know I’m mad?" said Alice.
"You must be," said the Cat, "or you wouldn’t have come here.”
- Lewis Carroll, Alice in Wonderland
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