“I noticed that Clark has a mole right above his lip,” Cat’s voice echoed in her head. “You never noticed that.”
Sure, Lois had. There it was, right above… Superman’s lip.
I knew really noticing the mole would destroy Superman's secret. I guess making sure people don't look at his face was crucial.
Lois raised her eyes to Superman’s and recognized the same deep pools that she had fallen into numerous times when gazing into Clark’s eyes. The only difference was a pair of glasses.

she knows.

she still loves him. ALthough she might still be mad about Cat. Hmm.
He does need to tell her more. Not that he really knows much more.
Except that there are lots of things she does not know. Also, some things she does know will not really add up.
Superman, Clark, whoever he was, smiled sheepishly at her. “I’m sorry, Lois, but I’ve got to go.”

that they did not talk more know. I guess that is why you had the intruder. Otherwise Clark would just need to stop Nightfall, and that would leave him a little more time to talk to her.
“Right,” Lois replied automatically with no conscious thought behind the words. “Nightfall.”
I guess explaning that an intruder had tried to kill Cat and then jumped from the apartment and he needs to report it to Henderson would be a bit much at this point.
“Will you be all right?” he asked.
Why bother asking, the last time he trusted she was alright, he clearly made the wrong decision.
She nodded slowly. How could she not be all right? Her boyfriend was the same man who had smashed her heart into smithereens,
I guess it makes sense this still hurts her.
the same man who claimed they could never have a relationship,
Well, that is because he sees himself as first and foremost Clark. Hopefully he will be able to convince her that he is Clark first.
and the same man who had disappeared at the same time as her boyfriend.
Now she knows why.
Lois set her hand over the hand caressing her face, and then touched his face with her other hand, running her thumb over his mole. “You’re right, Superman, one kiss changes everything.”
I wish she had said Clark here. However, I guess she does not yet realize that Clark is who he is, Superman is what he can do. Also, it would have made it too clear to use she knew what was up.
She had just cheated on her boyfriend with… her boyfriend.
Which makes no sense. Especially since he thought she knew it was him. They really do need to talk. However, I guess stopping Nightfall comes first.
Lois wished this development changed things. She wished that his one lie made everything all right, but the truth of the matter was that Lois had cheated on Clark.
And yet at another level it means that she has not even been tempted to cheat on her man since she first met him. She has never even been close to cheating.
Sure, it was with Clark’s alter ego, a flying superhero, but at the time that she had initiated the kiss, she hadn’t known that.
But he had no clue she did not know it was him.
All that she had known was that she was in pain from Clark’s supposed betrayal,
I am glad she now thinks of it as a supposed betrayal.
but that somehow Lex Luthor had acquired the power to hurt him,
I guess this is true. Although not in the way she thinks. Hopefully his memory of the boat and being underwater returns soon, so they are not over scared.
the ability to kill Superman,
He probably still has some kryptonite.
and Lex was doing this because of her.
Actually, with SM it is the other way around. His interest in her is caused by his perception she has a connection with SM.
Therefore, Lois would be the only person who would be able to stop Lex.
She might be right.