Another hint from this great fic? Later in the story:

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It had been a long day and she suddenly felt tired. All she wanted was to go upstairs, crawl into bed, and fall asleep in Clark's arms.

Standing at the foot of the stairs, she called to Clark, "Are you ready to come up?"

Clark faced her, standing absolutely still. "No, Lois. I'm staying down here."

"But, I thought you remembered everything."

"I do, but..." He wasn't sure how to explain this to her. "I'm sorry, Lois," he finally said very softly, "I'm not the man you want."

"But, I..."

"No, Lois. I'm not coming up." He began pulling out the couch and making up the bed.

Lois watched for a few seconds, and feeling an unexpected hollowness in her chest, she slowly forced herself upstairs.

Clark lay on the couch looking at the ceiling. He could hear the sound of the water in the sink, Lois brushing her teeth, and the sound of the occasional sniffle. He wished that it were still yesterday so that he could become Superman and just walk up the stairs and take her in his arms and tell her that it would be all right. Then he would lead her to his bed, and they could make love as they had the night before.

Instead, he was better. Right! he thought sarcastically. Now he knew that Clark Kent and Superman were one person, the one thing, the one person whom he wanted the most was out of his reach. She loved Superman, but that wasn't him.

She had been incredibly supportive of him, bringing him back to Smallville and helping him get better, but that was probably because she wanted to have Superman back. He was surprised that once she knew he was Clark, she still invited him up to her bed. Well, maybe Clark was the price she had to pay for having Superman.
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