Oh wow, after Hasini's amazing review, there surely isn't much to add. I'll just throw my two cents in....

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Even though you’ve been raised as a human being, you’re not one of them.
I hate this. It's all Superman II, the movie that defined Superman in such a way that I thought that I would never be a Superman fan again. Superman has to think of himself primarily as Clark, primarily as a part of this humanity which he is protecting. If he isn't one of them, if he isn't one of us, then he is elevating himself to a kind of godhood, and I feel convinced that only very, very bad things can come out of that.

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He had never felt so alone.
Exactly, Clark. Either you are one of us, or else you may as well leave the Earth and spend the rest of your days on Mars, for all the difference it will make when it comes to having friends and enjoying togetherness.

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He was tired. Fear had drained him, and instead of spending the evening with Lois—even an angry, focused, intense Lois—he was walking in the dark, a solitary man amidst humanity, but not a part of them.
No, Clark! Don't think that way. And don't dismiss Lois like that. So she doesn't like Clark Kent right now. Why is that? Have you been turning yourself into a more stuttering fool than you had to? You know there is no chance that she dislikes everything about you. She liked you as Superman, she adored you as Superman, even when you were injured and broken. There are things about you that speak so strongly to her, even now - so you must fight for her.

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He’d go home, order a pizza, and watch a mindless and light-hearted movie—preferably the most foolish and pointless one he could find. Maybe he’d even call Jimmy and see if he wanted to join him…
Jimmy. frown When I figured out that the extent of Superman's non-formal interaction with humanity might be Jimmy, I knew that this aloof Kryptonian held no interest to me any more.

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“Help, Superman!”

Clark’s hand flew up to his tie and he had taken a quick step towards the next shadowed alley before he stopped himself dead in his tracks. No. Superman wasn’t back. He was still grounded...

He didn’t care.

In a fraction of a second the wide-eyed, helpless expression evaporated from Clark’s face. His jaw tightened, and something flashed in his eyes behind his glasses.

He didn’t care.

Another moment, and the space where Clark Kent had stood was empty except for a sudden and seemingly unexplained gust of wind.

“Hhhhhhhhhhhhhhhhhhe—”

Clark ran. He ran like he hadn’t run in years, following the sound of the cry. Wind whipped at him, tearing at his work suit as he flashed beneath the dull glow of lamp posts and past sleeping shadows that blurred together into the night like a strobe light.

“—eeeeeeeeeeeellllllllllllllll—“

He knew his city, but even so it took him longer than he would have liked—precious seconds had passed that would not have been necessary, if he could have flown.

“—lllllllllllllp…!”
Sorry to quote all of this, but it's brilliantly written! You show so marvellously how time is stretched for someone who possesses super speed, how many things this person has time to do and how many thoughts he has time to think while an ordinary human is screaming for help. At the same time the woman's continuous scream is completely nerve-wracking, like being helplessly mired in sleep and being unable to completely wake up, even though your alarm clock is loudly, relentlessly beeping.

So Clark injured the man. I don't like it, but under the circumstances I can totally, completely forgive him.

And how wonderful this must feel:

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“It was a miracle!” the woman cried. “Just…this wind…and then…the knife, and then the man just…It was a miracle!”
It was a miracle... but Clark, you were the miracle. You were the miracle.

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He ran through drops of rain held suspended in the air, breaking them into shattered mists, and his face and clothes were soon soaked. His leg ached slightly from the strain, but he didn’t care.

He smiled.
Yes! Because he was able to help people again!

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Clark didn’t hesitate this time. He was ready.

With a burst of speed that put even his previous sprint to shame, Clark disappeared into the night, a light in his eyes that hadn’t been seen there for many days past.
There was a light in his eyes... I vividly remember the last time you told us about the light shining in Superman's eyes. That was in Lois's photo of Superman, when he looked so happy beneath a somewhat grim exterior, because he had probably pulled off several good rescues that day. Now the light in his eyes is back. Hasini called him SuperClark. I don't mind that name for him - I love it, actually - but I think that, when that light is back in his eyes, then he is Superman, for all intents and purposes. Welcome back, Clark Superman SuperClark Kent!

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It wasn’t the pair of stilettos she had worn in the White Room, but they were enough to remind her of it anyway.

So many things did. Simple things—little nothings. The soup kitchen on the corner not far from Lois’s apartment. A man wearing a jacket just a bit too red.
So poignant....

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Dark eyes, because they were like his, but not. She would never be able to find anyone else with those innocent, hurt, burdened, selfless dark eyes.
And this - I completely love it. Really, I don't want to make this uncomfortably religious, but when you think of it - doesn't Lois think of Superman in a way that reminds you of the suffering, sacrificing, giving and loving Christ? (Eh - how long was it before Superman disappeared from Lois's apartment? Three days?)

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When she walked outside and saw that the day was cloudy, she worried that he wasn’t getting enough sunlight.
I love this, too - how Lois associates Superman with sunlight.

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She drank coffee and thought about him, with his overdose of sugar and cream. She tried to drown herself in chocolate and she thought about him. Coffee. Cream. Sugar. Chocolate. Raspberries. Red. White. Black.
And I completely love how you write this. Coffee, cream, sugar, chocolate and raspberries are things that taste good and most of us like and want. But consider the colors of these things, too. Coffee is black, cream and sugar are (usually) white, chocolate is dark-colored and raspberries are red. Like the colors that haunt her: the white room, Kal-El's white face, his bottomless suffering black eyes and his red blood.

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He was everywhere.

Grass. Sky. Pain. Content. Boredom. Fear. The sun. Darkness. A child crying. Someone laughing. Clark Kent . . .
So beautiful. It reminds me of what my mother said about Jesus, too - that he is everywhere and in everything, though we can't actually see him. (I didn't necessarily believe her, but it was a beautiful thing to consider.)

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Her thoughts pulled to a sudden stop.

Clark Kent?

Lois’s lips turned downward in a frown as her partner’s face popped into her mind. What was that about?

She hadn’t even had time to really think about Clark Kent. Of course he reminded her of Superman—she’d been over this before. He and Superman had been friends, so somehow her mind made that connection and the slightest hint of Clark Kent warned that Superman was close behind.

Lois shook herself. Clark Kent was another matter, entirely apart from Superman.
I'm getting slightly tired of Lois by now. She spent so much time scrutinizing Kal-El's face during their captivity, and she has, of course, spent a lot of time with Clark Kent. Why is she so totally unable to see that they are one and the same man? Given the circumstances, she should have suspected that they are the same man even if they had actually looked quite different - which they obviously don't.

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When it came down to the luck of the draw, when everything seemed at a loss, she seemed to have pretty good odds. She would never bet against herself, certainly, with her record. She might have bad luck getting into trouble, but she always managed to get out of it, no matter how dire the circumstances.
I love this. Lois would never bet against herself, because then she would probably lose... what a wonderful way of describing her ability to survive the tight pinches she kept getting herself into.

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The problem wasn’t fate, necessarily. It was people. Someone had targeted her, and targeted Superman. Someone who was still out there.

Someone who could put Lois Lane on fate’s bad side again.

There was a knock at the door.
Someone already pointed out - Symbolicangel? - that the way you manage to charge these three sentences with foreboding is amazing.

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Lex stood there in the growing shadows of the evening, holding a large bouquet of deep red roses.

A little bit too dark red, Lois thought.
Yes. Red like blood, I'll bet.

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Lois took them. Their scent wafted up towards her. They smelled like new rain and clean ocean—like the air above Metropolis, when she flew with Him.
She flew with Him! Is she associating Superman with Christ or what?

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“You moved your couch.”

Lois grimaced, allowing the change of subject if Lex so wished it. She still hadn’t moved that uncomfortable thing from its place by the window, where it had been when Superman had been sitting in the sunlight, his eyes gentle as he watched her…

She actually intended to get rid of the couch completely and get something more comfortable, but she had been too busy, and she was strangely reluctant to give the awful piece of furniture up.

“I just…was reading and wanted to see the sun yesterday, that’s all.”
This is really ominous! He is really saying, 'You had Superman here and he was soaking up the sun, right?'.

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“I’ve dealt with big stories before,” Lois said calmly. Lex still watched her, as if waiting for more, and she continued, “besides, I do have a partner.”

Lex sat back, wearing a slight frown of disapproval. “Ah, yes. Clark Kent.”

Lois didn’t like his tone of voice. “Yes, Clark Kent,” she affirmed.

“Considering your elite status among reporters, I am still astounded that Mr. White would put you with someone so inexperienced.”

“Clark isn’t that bad,” Lois said, almost defensively. “He may be experienced, but we all had to start somewhere. He has a good heart, and he’s one of the better writers I’ve come across.”
Small typo here... you want to say that Clark is inexperienced. But I love how Lois automatically defends Clark.

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Lois took Lex’s offered arm again, and they walked forward into his expansive mansion. The large halls echoed emptily with their steps, but as they entered a dining room soft classical music filled the silence with sound. They were soon seated at a table set for two, with no sign of propriety neglected. Soft classical music drifted from the corners of the room as they began to eat.
Big, empty mansion. No one and nothing is there for her, except the cool, elegant, classical music.

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Lex smiled at her. He had hardly touched his food, while Lois, contrarily, had downed the first and second courses in almost astonishing speed, even while she had made a special effort not to eat like a starving woman.
There is definitely something wrong with Lex.

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“Oh, yes. LexLabs just signed the deed official—we will be incorporating Metro Physics into our facilities. Our science branch will increase by 30% initially, and soon, my dear, we will no doubt have resources like none other on the eastern coast for the betterment of science and medicine.”

Lois felt her heart choke briefly within her, but outwardly she casually lifted her fork and lifted a bite of dessert—the most heavenly, rich chocolate mousse cake she had tasted in her lifetime—to her mouth. She took her time as if savoring it, but in truth she barely tasted it.
Metro Physics? Now that rings a bell.

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Lex smiled. “Indeed. As the tide of the sea changes with the passing of the moon, so is the rise of empires.”
What about the fall of empires, Lex?

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Prometheus Project.

C.O. MP murdered.
MP - Metro Physics, right? C.O. - would that be C.E.O.? (I'm having trouble with your English and American abbreviations.)

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What if…

What if Clark Kent was right after all?

After demanding herself to be foolproof, could Lex Luthor have been hiding just under her nose the whole time? Or was she just getting too paranoid?

No. Right now she couldn’t be too careful.

Or maybe, possibly, it was just a coincidence.

Maybe.

But that didn’t explain why her reporter’s sense was suddenly going haywire.

She didn’t know how she could find any more information that might point towards Lex’s involvement in any robberies or illegal research, as Clark claimed . . . and especially not that nonsense about aiding terrorists in Iraq. Besides, why would Lex worry sabotaging tsunami warning buoys in New Zealand? So even if Clark was right about some things, he certainly couldn’t be right about everything.

Could he?

No. Of course not. It was ridiculous.
Oh. Oh. Oh. This is so damn scary.

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Had she walked right into the serpent’s lair unknowingly?
Yes, Lois. I really think you have.

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A picture of a scene from Dante’s Inferno brought Lois up short. It was a gruesome scene, depicting certain levels of the descent into Hell—from men standing in boiling blood or lying on burning sand to those sinners lying disemboweled or infirm, yet eternally alive in their anguish.
Dante's Inferno - how appropriate.

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Lois’s eyes drifted down the terrible scene, until her gaze stilled upon the furious apparition of the three-headed devil, the red flames of eternity reflecting off his bare and hairless heads as he stood, tall, terrible, and triumphant amidst his horrible kingdom.

Lex Luthor was created in Hell, and is commonly known among his peers as the oldest son of Satan, also known as Lucifer…
So Lex is the son of Satan, and Superman is the Son of God? No, not quite, I guess, but... yes, you make me think along those lines.

Interesting. And in the beginning of this post, I said that Superman mustn't elevate himself to godhood, yet here I think of him in some ways like a modern Christ.... Ah, but these things are not necessarily incompatible, and in order to be truly, truly good, you must be the Christ who doesn't elevate himself to godhood.

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C.O. MP Murdered.

Illegal experimentation.

B. 39.

Experimentation…

Bureau 39…

Her guide had seen Lois stop, and was now droning on about the history of the painting before her. Lois didn’t hear him. The walls were closing tight around her, despite the high, shadowed ceiling, and her hands shook as she pulled her sweater closer around herself.

Bureau 39.

Lois swore mentally, panic creeping up her back. What if Clark was right about that too? What if she had walked right into another trap?

No.

Experimentation. Kal-El. Bureau 39. Lex. Superman. Luthor. Clark Kent…
Oh, damn. This writing can't be good for people who have trouble with their blood pressure.

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He had been watching her. He had known who she was, and that she had hid Superman.

This was worse than fearing she might be caught by the Primaries earlier that day. She had been ready then. Now, her throat had closed in on itself and she felt like she was suffocating.

Lex knew. He had seen everything.

She needed to get out of here. Now.

Superman…

No! She couldn’t call him. She couldn’t call him. She couldn’t .

Her fingernails dug into the palms of her hands painfully.

No. No! She could do this. She had to do this.
Oh, no, no, no, this is almost illegally scary....

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They went out onto the balcony, and Lois immediately felt better at the sight of the stars reaching down around them. It didn’t last long, though, because she knew how it felt to truly fly amongst the stars, and there was only one man on Earth that deserved that sort of power.

Had Lex always tried to put himself at Superman’s level? He had raised himself so high, and brought Superman so low…

Where was he?
Hmmm. You really show us Lois as if she was standing between heaven and hell, between Christ and the Devil.

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“It’s…beautiful,” she said simply, stepping to the balcony edge and away from Lex. The tightness in her chest eased slightly, even though Lex followed behind her.

“Isn’t it, though? The most beautiful city in the world, and here we are, on top of it all.” Yet despite of his words, Lex sounded strangely melancholy, and he finished with a sigh as he ran his hand through his thick curly hair.

As he drew his hand away, however, thick, dark strands stuck to his fingers like webs. He stared at them for a moment, and his fingers rubbed the hair together as if he were checking to make sure it was real.
Thick, dark strands stuck to his fingers like webs... like spiderwebs... like tiny snakes! So horrible!

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“Lois,” he said, his voice soft but dark. “I have a condition that is extremely rare, and hardly studied. Commonly speaking, the closest you may have heard of it would be…cancer.” Pure loathing seethed through his words. Disgust.
Did he get his condition from handling Kryptonite, perhaps?

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“My condition was not good. Until two days ago I was bedridden, and we thought the worst.” He paused, looking over at her. His eyes lingered on her like a touch, and he smiled, but it didn’t reach his eyes. “All is not lost, however. With research my doctors have discovered a type of radiation treatment, and with a slightly altered version of the usual attack against such illness, we have good hope for full recovery.”
For some reason, I completely shudder at this. I keep thinking of those "samples" that Lex's goons took from Superman in the white room. Are Lex's doctors going to transplant them into Lex's body? If you are going to take your story down that route, Rachel, please don't make Lex end up stronger than Clark. That doesn't make sense, in my opinion. Clark has most of himself, of his own body, but Lex has his own sick body and, at best, a little bit of Clark's.

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She wasn’t sure—she certainly didn’t have all the facts—but impossibly, incredibly . . . Lois couldn’t help but realize that Clark was right. Clark had been right all along.

Her newbie, inexperienced, naïve partner had been right. She had been wrong.

How could she have been so blind to Lex Luthor’s true character?

How could she have missed the signs?

Lois felt as cold as ice, and vulnerable. She went back to the main room and grabbed her high heels as she went into her room. She turned on the light and looked around, shaking as she looked around.

Lex had asked so casually about Superman, but he had already seen it all. He had the tapes. He knew everything.
I love that Lois is realizing this.

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Her warmly-painted room felt cold as white. The soft light of her bedside lamp was normally soothing, but now Lois only felt detached. Separated.

Alone.

Superman had almost died. He had left her.

Her parents…

Bureau 39…

Lex…

Clark…

Superman…

Fear. Hope. Pain. Comfort. Hate. Love. Agony. Terror. Laughter. Screams.

Alone…
How beautifully written, and I love how you use the word "alone" twice, to such great effect.

Let's remember, too, that in the beginning of this chapter Clark was feeling unspeakably alone. These two people need each other so badly.

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Without warning, the floodgates opened, and tears that she had been fighting furiously for what seemed like a lifetime poured out in great sobs.

Lois collapsed on her bed, her body shaking as she found herself helpless against the unexplainable tears. She curled in on herself, feeling cold, furious, so afraid, so alone . . .

“Superman,” Lois choked between her tears, hugging herself as she shut her eyes against the world. “K-kal-El. Superman. I really, really need you right now. Please. Please. P-please. S-superman...”
Oh, I feel so, so sorry for her.

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Lois bit her lip, wiping her eyes again and searching for that anger, but finding that it was strangely dissipated. She had found him--Lex--the Boss. After that first puzzle piece had fallen into place, the rest had slipped in, and Lois now had no doubt.

She took a deep breath, drawing up what little strength she could around her. In the dim, artificial light of her apartment, Lois stood as a pillar.
I totally love that image - Lois stands like a pillar. She is a slight woman, slim and moderately short. But she is so strong, and in her own way, so pure. She is so completely ready to fight the devils and demons, like a Joan of Arc, as I said before... I love it.

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Clark…

Once Lex Luthor was in jail, maybe Clark would go back to how he was before this Bureau 39 fiasco. He hadn’t been that bad before. Just a bit naïve. Now, though, his awkwardness was more than a little annoying.

And he had seen through Lex Luthor, even when she hadn’t.
Oh, Lois. Please don't be so horribly contemptuous of Clark.

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She turned off all the lights in the house, but left a lamp on by her bed as she crawled under the covers. She reached over and drew a bundled length of bright red cloth from under the covers on the other side of the bed and cuddled it close to her chest. She buried her still tear-flushed face in the soft fabric, as if searching for the scent of the man that had worn it, not too long ago.

Superman.

She had tried to get the stains out of the cape. She had tried to mend the holes. But the stains had stayed, and the color had faded where she had scrubbed at the awful dark spots, but in vain. The holes were just hopeless. Lois doubted even Superman would ever be able to fix it up again.

Besides, it wasn’t as if he was asking for it back, Lois thought as she spread it out and wrapped it around her shoulders.

In it, she felt protected. Safe.

Not quite so alone.
Oh, I love this. Lois wrapping herself in Superman's cape, feeling a little less alone. It reminds me of people who collect relics from the saints. In a way, Lois could have been wrapping herself in Jesus' cloak.

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Despite the still-lingering cloud of tears, Lois couldn’t help but smiled slightly at the open, honest tone of Clark’s voice
I love how his kind voice makes her smile. (And there is a small typo - Lois couldn't help but smile.)

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“Hi, Clark. This is Lois. I just…” She just what? Now she just felt foolish, and even more pitiful than before. She was glad her partner couldn’t see the mess she was right now. “I—I know you were worried about me going with Lex. Well, I’m back, and I’m fine. So no more need to worry, okay?” She paused, then sighed. “Sleep well, Smallville.” She ended with a soft tone that surprised herself as she hung up the phone.
I love her soft tone!

Oh, please, Rachel. Lois and Clark so desperately need each other right now. Please, please, please let them get together.

Wonderful chapter. Wonderful story, Rachel!

Ann