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Clark did not close his eyes that night, and when the sun finally rose above Metropolis, he was sitting in the window seat of his apartment, still holding his torn and filthy cape. It was a gray and dismal dawn; banks of heavy clouds had rolled in from the bay overnight and now hung ominously over the city.
There is something about how torn and flthy Superman cape is so much like the gray and dismal dawn: like the dawn, his sullied cape is so imperfect. Like a too-rainy day. For me who live in Sweden it is easy to sympathize with people who complain about the rain, because I know what it's like to get too much of it. But then, where would we be if we got know rain at all? What would we be, if we got no rain at all? Extinct is what we'd be. Face it, Clark. There is no such thing as perfection.

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That single moment when he'd held Lois in his arms and recklessly decided to jettison Superman from his life seemed to taunt him with its remembered perfection.
Well, yes, there is perfection... but only in very small doses.

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She deserved that life, and he couldn't offer it to her. In a few hours, she would know it. All his lies - his years of deception - would be laid bare before her, and what sort of future could be built on such a weak and rotten foundation?
Well, as long as you abandon the rotten old foundation of lies and deceit, offering Lois a new foundation of honesty and trust wouldn't be a half-bad thing to do, if you ask me!

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“You didn't think I was actually going to let you do it, did you?” Lois's voice came from behind him, low and controlled.
Oh wow! Wow! Caroline, I hadn't expected this!

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She took a step closer to him, and he closed his eyes, wishing the earth would open up at his feet and swallow him – anything to keep him from having to face her like this. He had a hundred questions, but he was afraid to ask them. Afraid of what the answers were going to be. Afraid of Lois and the fury that seemed to be radiating off of her in waves. He was the strongest man in the world, and he was terrified of this small woman who had a death grip on his heart.
I love how you write this, how you use your word magic to make us see what we have learnt to express in much coarser, sloppier terms, that Kryptonite has got nothing on Lois.

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“You said you would,” he said stupidly.

“I lied. You know all about lying, don't you?
Oh, wow. Touché.

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“That's interesting,” she said. “Because here's the thing: I might be stupid enough to be fooled by a pair of glasses for two years, but I'm not so stupid I don't recognize my own partner's writing when I see it. You didn't discuss this with Clark, and yet I would stake my career on the fact that Clark Kent wrote this press release. What should I make of that, Superman? What exactly does that mean?”
This is a brilliant revelation. Of course Lois, the award-winning reporter, must recognize her own partner's writing style.

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“The other night, you knew about the fire, didn't you? You knew about the fire, and instead of going to help, you were making out with me on the couch.”

“I'd promised you I wouldn't run away again. I'd promised you…”

“Don't you dare blame this on me!”
The horrible thing is that she is right. If someone had died in that fire, Clark subconsciously would have blamed that person's death on Lois. Because it would have been her "fault" that he couldn't come to their rescue.

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“When was I supposed to do that, Lois?” Suddenly, out of nowhere, the anger rose up in him and poured out in a white-hot torrent. “In the early days when you'd have splashed it all over the front page of the paper? Or maybe when you were getting ready to marry the most dangerous criminal this city has ever known? Would that have been a good time? What about the day you handed me back my heart and then threw yourself at Superman? Should I have told you then?”

“Yes!” she hissed. “Any of those. All of them. Anything would be better than this.”
I don't agree with Lois that Clark might just as well have told her right away, pretty much as soon as he met her. He had to get to know her first and find out if he could trust her. But personally I don't feel sorry for Clark for being rejected when he asked Lois to love him as Clark Kent. He was lying to her then, not about his love for her, but about himself. He didn't deserve her love at that time.

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“'Even if you were an ordinary man leading an ordinary life.' That's what you said to me that night, Lois. That even if I had no powers at all, you would love me. Do you have any idea what those words did to me?”
It's strange how he keeps coming back to Lois's misguided answer again and again and uses her reply to him as a kind of justification for his continued lies to her. Lois answered as a person who had been well and truly deceived, because he had well and truly deceived her. And to him that was proof enough that she was untrustworthy and that he had to keep lying to her?

In a previous part, Clark told Constance Hunter that the woman he loved needed him to be two people. I think that is as far from the truth as it could be. It was Clark who needed to be two people. He needed to be perfect farmboy-reporter Clark Kent on one hand and perfect superhero Superman on the other. Mentally, he split himself in two. Then he successfully fooled Lois into believing in his charade - and suddenly, he could project his own need to be two people onto her. He needed her to love a man who didn't exist, but that he liked to pretend that he was - non-superpowered Clark Kent. And then he made himself believe that he was fooling her for her own sake, because the truth would be unacceptable to her. And therefore any problems he had because of his double life could be seen as something he himself was suffering and sacrificing because of Lois.

Once again, his own problems were Lois's fault.

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“Do you have any idea what it did to me when you let me think you were dead?” she spat back at him. “I was imagining my best friend's body full of bullet holes, tossed in a ditch somewhere, and all the while you were flying around playing hero. Did it ever once occur to you then to tell me the truth?”

“You have no idea what I went through then,” Clark whispered. The memory of that time seemed to claw at his insides, somehow tied up with those boxes in his apartment. Either way, Cark Kent dead and gone, and nothing left but Superman.
Suddenly, you made my breath hitch. Yes, being hit by bullets and having to pretend that Clark Kent, the man he needed to be, was dead, and being unable to think of any way to get him back, must have been inconceivably horrible. (And I don't know if I've told you so, but that metaphor of packing an entire persona away in boxes is simply brilliant.)

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“No,” she said, and all of a sudden the anger seemed to drain out of her, only to be replaced by something much worse – much more painful. “No, I don't have any idea what you went through because you never trusted me enough to tell me. You never once let me see you. You just lied and lied and lied some more. And now this.” She indicated the press release. “You're not doing this. Not for me.”
So raw. So true. So painful.

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“Last night… there was a baby…you probably saw it on the news, I don't know. But he was wrapped in a newspaper. Wrapped in our newspaper. I found him, and I realized I couldn't… that Superman had to… stay.” He paused, realizing that he wasn't making any sense, but he couldn't explain it any better than that. “I can't keep the promises I made to you, Lois. I can't offer you a normal life. I thought I could do this… that I could be free. But I can't. I love you… but I just…”
But he still doesn't understand. He seems to be apologizing for not being able to give up Superman for her.

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“Lois,” he pleaded, hardly knowing what he was asking for – just knowing that he needed her not to leave things like this. But she shook her head.

“I can't do this now. I can't talk to you... like that.” She gestured at his suit. “I don't even know you like that.”

“I'll change,” he said, hearing the desperation in his own voice. “It's just a costume, Lois. It's always been just a costume.”

“But who are you, under that costume? That's what I spent all day yesterday trying to figure out. And I never could.”

“You know who I am. You know me.”

She shook her head. “The man I thought I knew....” Her lips trembled and her eyes filled with tears. “The man I thought I knew wouldn't have done this to me. Not Clark. Not my best friend. He would never have lied to me about something so important. He wouldn't have made a decision like this without telling me.” Her voice tore on a sob, and he was sure the sound of it was more painful to him than Kryptonite.
I hope he heard her this time. I hope he realizes that he will have to give up his old foundations of lies and deceit and offer Lois honesty and trust instead. Because if he won't, how can she know him and trust him?

It's quite interesting that you had Constance Hunter see and hear Lois and Clark/Superman's argument. I very much like her intervention and her suggestions to Clark:

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“You should go after her.”

“No,” he said dully. “You heard her. She'll never forgive me for this.”

“I didn't hear her say anything like that.”
Indeed, Clark. She didn't.

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For the first time in his life, he didn't care in the slightest that someone had probably just learned his secret. He turned to her and held out his hand. “In fact, I'd like to introduce myself. My name is Clark Kent, and I'm Superman.”

It sounded ludicrous, as if he were beginning a twelve-step program for recovering superheroes
I snorted at this. Like Lisa, I was immediately reminded of Mr. Incredible.

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as he said the words, he felt as if a giant weight was lifted from his soul. My name is Clark Kent, and I'm Superman. He should have said those words to Lois long since, but he wasn't sure he'd completely believed them himself until the night before in the alley, when he'd held that small, discarded life in his hands. In that one quiet moment, something had been reconciled. Something had been accepted. And now he could say the words and mean them.
Yes, he himself had needed to be two people. But now, finally, he could accept that he wasn't.

And Clark went back to the hospital, where he was welcomed by all. It was a nice touch to let him be greeted and shown around by a nurse who reminded him of his own mother. Again, the similarity between himself and the little foundling boy is driven home.

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Clark approached the bassinette and looked at the child in wonder; such an amazing transformation in a few short hours! He was pink and healthy and sleeping soundly, innocent of the fact that his arrival to the world had been in any way unusual.

Katie scooped him up and placed him in Clark's arms, and he turned slightly away from her when he felt tears prick his eyes. How embarrassing, for Superman to be getting choked up over a baby.
Not embarrassing in view of the fact that this little boy reminds Clark of his own miraculous salvation.

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Katie left them alone then, and he sighed deeply and settled the baby more comfortably as he rocked them slowly back and forth. Maybe it was the tight swaddling, but Jonathan felt more substantial to him now, his weight and warmth in Clark's arms a solid, comforting thing.
The way you write Clark's incredible bond to this little boy has me wondering if you will find a way for Lois and Clark to adopt him. (Yes, because I really don't doubt that you will make Lois and Clark find their way back to one another and build a new life on strong, solid foundations of honesty, love and trust.)

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And he needed that comfort. The memory of Lois's face, shattered and hurt, was a constant torment. He would never forget the moment she told him he was not the man she'd thought she knew. It was worse, somehow, than anything he had feared, and the worst of it was that he had no defense. How could he expect her to have known him when he hadn't truly known himself?

“My name is Clark Kent, and I'm Superman.”
He didn't know himself before, but now he does. And he is beginning to see how he must offer Lois his true, undivided self if he wants to respect and honour her.

Great, Caroline! Please don't make us wait long for the final part.

Ann