Well done again Sara, a very intense section which had some great character insights and some back-story exposition.
Lois shut her eyes and shook her head violently. Nightmare. It was just a nightmare. She wasn't really here. Not again.
Not. Again.
And what they were going to do to her now. It was the same thing. All over again. Only it was worse. This time they'd be mad, furious that she'd escaped. They'd tor-
The mental torture that Lois is experiencing shows the heightened state of panic she is currently experiencing. The short sentences convey how fast these frantic thoughts are going through her head.
But... she wasn't alone. At least this time she wasn't alone.
With Clark’s cough she remembers he is there as well. His presence functions as a stop-gap measure to keep her panic from becoming a full-blown hysteria.
Even with Clark there, she still shuddered at the thought that someone had gone to so much trouble to recreate an exact replica of the cell she'd been kept in for years in the Congo. Whoever had done this was evil and sadistic in ways she couldn't even fathom.
*cough* Luthor *clears throat*
But he hadn't shared, not until she'd mentioned it. And with two little words, he'd made her doubt what little trust she'd had. If he hadn't told her, there'd been a reason. Like maybe he couldn't be sure which Lois he loved. Like maybe he'd loved *her* more and was just settling for what he could get back in his own universe.
She struggled with that idea, though. Not just because she didn't want it to be true, but because something inside her told her it wasn't. Even so, she still couldn't trust him. Or herself. She didn't know how love was supposed to work. Every time she'd asked in the past, people had told her she'd "just know".
These two paragraphs show very well the trouble Lois is having figuring out why he didn’t tell her about the other universe. I am glad that she rebels against the idea that Clark is settling for her. Clark experienced so much pain with the whole ordeal of universe hopping that he just wanted to forget all about it. I am curious to see how Lois reacts once she understands the whole story.
Well, she didn't just know. Or maybe she did, and she couldn't trust it to be real. Her days of jumping in without checking the water level were gone. She couldn't afford the risk... especially not with her heart. Not when she was so unsteady and damaged. She couldn't be sure that he'd be there for her if she fell apart again, not when he was just as fragile... and mortal.
This touches upon the heart of the issue in a very poignant manner. Lois essentially had her life stolen from her, and she is still struggling to get it back. She is not the same person she once was, but at the same time, in some ways she is the same. Keep in mind, I’m operating under the assumption that this Lois had similar earlier life experiences as the Lois with which we are more familiar. She is still building walls around her heart to keep herself from getting hurt.
And now a bit from the Pete/Elle side:
He'd gotten involved the moment he'd found Lois Lane's backpack in a storage closet eight months ago. That decision had jeopardized the entire operation. Not only had he lost his position as a valuable insider, but he was now considered AWOL. The ATF would suspend him if they could find him.
Hmm… So it seems that Pete was the one to help Lois escape. Very interesting. I am eager to see how the meeting goes and what happens when Lex shows up.
As I said before, I am really liking this story. Have you considered posting on Mondays and Thursdays again?
Just a thought

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-Em