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“I’m Clark Kent,” Clark said at the same time that Lois said...

“He’s not Superman.”

“Oh. Oh... Uhh... I guess I just never heard any denial so I thought... But that was foolish of me."
Ah, Dr. Klein! You have focused on the nub of it. You're not foolish at all. Of course Clark wouldn't deny it. Superman doesn't lie.

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“Today we’re asking ordinary people for their reactions to the revelations about Superman living with his super strumpet.”
/spits coffee across keyboard/

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“Marry me, Clark,” she said. “We could go down to City Hall today and just get it done. There’s no waiting period or blood tests required in New Troy. This will all go away if we just get married.”
Actually, I see this as very in-character for Lois. There's a problem, she's leaping in to solve it. I would, however, like to see the two of them discuss this, and have Clark think about some of the things that the other posters have mentioned.

And by the way, what did Lois find on the tape from Bill Church's room?