A bit of FDK here, Rachel, although there will be no Biblical comparisons this time (at least I don't think so at the moment....)

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He loved her, but at times she seemed to downright loathe half of him—the half of him that was him.

He didn’t want to be Superman, the Alien. He just didn’t think of himself that way, even if Lois claimed that she could see the person—the human underneath.
I think Clark is selling Superman short. He is a bit in denial about his superhero persona, refusing to see that this superhero is himself. (Though I must admit that Clark may be less in denial about himself than Lois is in denial about Clark.)

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Lois. She loved Superman so much, but after hearing her rant Clark had to admit that Lois did indeed have a point. In her eyes, he really was a cowardly, bumbling, stuttering, and irresponsible hick from Smallville. And as of late, had he given her any reason to think otherwise?
I'm glad Clark realizes that Lois has some kind of a point. (But I feel very sorry for Clark, too. Like you said, Rachel - being told these things about yourself isn't exactly going to make it easier for you to turn yourself into a better person.)

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And wasn’t that the worst thing of all? If once Lois found out, she realized that the real him—the whole him—was just too annoying to put up with?
Will she or won't she? As Tank put it a while ago, will Clark Kent be raised up in Lois's eyes when she learns about his Superman identity, or will Superman sink lower in her eyes? That's the sixty-four thousand dollar question.

But what about the pocketknife?

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She had found it for him. She had contacted the Primaries, and had probably taken McPheron by the throat and shaken him until he had begged mercy and gone out to find it himself.

But what was it supposed to mean? Was this just the beautiful, lovely, kindly angel peeking through a crack in the fortifications around Lois Lane’s being? Would she have done this for anyone? Or did she actually care enough to get the knife back for Clark Kent?

He didn’t know. Considering her fiery wrath, the thought that she would do anything for Clark Kent after he had disappeared on her yet again was astounding. So confusing. So unreasonable . . .
The idea that Lois would do anything for Clark Kent is simply wonderful. I want to believe that some part of her realizes that, yes, Clark is the man that she loves, or at least he is an aspect of the man she loves, and she just can't live without him.

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The sky was yet clear, though the eastern air from over the bay carried the blue scent of coming rain.
Sometimes your imagery is breathtaking in the humble simplicity of its originality, and in its perfection.

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He had landed and taken off a number of times since then, even with only the three rescues he’d helped with that night . . . but every time he looked up to the sky and the distantly twinkling stars he was afraid that when he tried to reach them . . . he wouldn’t be able to. That his feet would stay grounded.
You manage to give the word "grounded" a whole new meaning.

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The thought scared him so much that he was loathe to land time after time, for fear that he wouldn’t be able to break away into that true freedom once again.

Clark spun into the suit. He looked up into the sky again, and with a moment’s hesitation more, he took a deep breath and stepped out of gravity’s grasp and into the gentle air.
Beautiful....

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It greeted, him, the almost-unnoticeable wind currents brush against his skin like hands welcoming him home
Breathtakingly beautiful.

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He turned his face to the stars, letting himself drift upwards rather than drive himself forward through the perfect black air which sat silent like a flawless, serene, eternal river. He rose up, the world shrinking beneath him as he slowly picked up speed—faster, faster
Beautiful. Vertiginous. Mindbogglingly fraught with exhilarating rollercoaster fright. Like falling upwards, as if gravity was reversed, making you fall and plunge away from the Earth until your home in the universe disappears behind the event horizon of the cosmos, leaving you stranded in nothingness.

Well, you show us that Clark isn't scared of this falling away from the Earth anymore. He had only been scared the first time it happened to him.

But there is something symbolic about Clark's falling away from the Earth into space. Is it his alien roots calling him?

Clark doesn't continue his journey away from the Earth, however. He stops and contemplates his adopted world:

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It was such a beautiful world, he marveled. So large, so open and diverse—so expansive. He slowed slightly, letting the babble of the flowing brook of humanity glide through his ears, and through him.

The sound of life. The sound of love, of hope, of joy. Of being.
He loves it. He doesn't want to leave it.

But then he is assaulted by the cries of pain and fear. Trying to escape them, he flies higher:

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Trying to shake the sounds from his being, Clark drifted higher, floating out of earth’s atmosphere into the perfect silence of the vacuum of space. It was black there. Empty. The world sat beneath him, appearing almost lifeless as it floated there in the endless void of nothingness. He hovered there for a moment, directionless, then shivered at the cold he could almost feel.
The astronomy buff in me insists on pointing out that the world would look living and amazing from this relatively close up. If you could see the Moon and the Earth simultaneously (i.e., if none of these celestial bodies were located in the direction of the Sun from your vantage point) you would be struck by the visual difference between the Earth and the Moon. The Earth is much bigger than the Moon, but above all it is brimming with vivid colors, while the Moon is a dull, dark, almost monocolored gray.

And Clark doesn't like the silence of space:

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The silence was a thousand times more thunderous and chilling than even those countless pitiful cries for help. For in those cries there was life. There was hope, if only the vestiges of it clinging to despair.
So beautifully put.

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With those cries he was never alone.

He dove back down, the sound barrier cracking behind him again as he shot as blue lightning into the heavens down back to Earth. Thunder shook the air behind him as he shot between the buildings of Metropolis.

There was no hiding anymore, and there was always something for Superman to do.
I love it. The reverse gravity of his alien ability flight made him fall away from the Earth. The beauty of his adopted homeworld made him stop to contemplate it. Its cries for help made him, momentarily, fly away even higher to escape those sounds. But he really couldn't live without them, and in the end, it was those cries for help - and I guess, the hope those cries symbolize, because if there is no hope there is no reason to cry out - it was those cries that made him return to the Earth.

Beautiful. Beautiful. The only thing that would have made it even more beautiful to me is if Clark had also been aware of Lois out there in space, and realized that he nothing in the universe bound him stronger to a place than the presence of Lois Lane, and his own desperate need to be with her.

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Superman angled down, x-raying quickly to get a picture of the whole situation. With a last burst of speed, he dove downwards, catching the four bullets that were hovering in the air as he swept past. The window to the store was already broken, so foregoing the door Superman flashed inside, slowing only enough so the glass fragments wouldn’t get caught in his current of air and become deadly projectiles. He stopped abruptly, landing on his feet as his cape caught on the wind he had created and billowed out behind him.
What a wonderful description of the awesome power of our favorite superhero.

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Clark flinched, but caught himself fast enough that he didn’t move, not even a change in his expression.

The gun went off, and then again. The bullets flew slowly towards him, and he watched them as they almost seemed to drift, spinning lazily in the molasses air as the sleek metal lulled towards him.
Beautiful. You make us see things through Superman's eyes. This is what the world would look like if we, too, were faster than a speeding bullet and physically invulnerable. At the same time you remind of of Superman's mental vulnerability, his fear.

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Suddenly, one of the officers searching the crook straightened, cautiously drawing from the man’s pocket a short, thin, sickly-green colored crystal.

Rational thought fled. Clark staggered back, bumping into one of the police cars and sending it a good two feet backwards. The side window shattered as the door bent in from the force.
Oh, wow! You scared me to death, Rachel! And I'm still inside Clark's head, still seeing the Kryptonite-colored crystal through Clark's eyes, feeling his panic because of it.

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Henderson swore, coming forward. “Are you all right?” he demanded.

Clark swallowed, hiding the shaking of his hands by continuing to brush the fragments of glass from his cape. “Yes,” he said, his voice as steady as he could make it, despite the scare.

Henderson swore again. “We had heard that this stuff—this kryptonite-could hurt you, but we never actually believed.” He turned and barked, “You men! Get that contained and put away for analysis. I don’t want a single speck of dust left behind, understand?” He looked back to the superhero.

It was dark, so the hardened police chief may have imagined the slight flush of embarrassment and shame that crept over Superman’s pale-colored face.

“I really am all right,” he said, looking up at last. “That . . . that wasn’t—isn't—kryptonite.”

Henderson frowned at him, recognizing the honesty of his tone. “But then why . . . ?” His sentence trailed off and he stopped, looking at the superhero with a new light of realization in his eye. “You thought it was kryptonite.”
Oh, wow. Henderson is smart and sharp-eyed. And poor Clark, the shame of having revealed his fear and weakness in front of Henderson. Well, now it has been confirmed - Kryptonite is real, it can hurt Superman, and it had something to do with Superman's disappearance.

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“Superman, have you talked to Lane yet?”

Clark frowned at the unexpected question, and his eyes narrowed. “Why?”

“She’s been in contact with an organization called the Primaries.” Clark looked at him sharply, feeling a chill. “They came to me some weeks back, asking me to join up with them, seeing as I had talked to you more than most.” He paused, glancing up to make sure no one had come close enough to hear. “I turned them down.”
Gaahh!!! This sounds bad. The Primaries seem very bad news, now. And Lois was in contact with them, to retrieve Clark's pocketknife.

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Henderson nodded. “Good to have you back, Superman,” he said. There was a pause. “Be careful.”

It was the first time anyone had ever told him to be careful while he was in the suit, besides his mom and dad.
Got to love Henderson. He is a kind of surrogate, if distant, father to a lot of people, I think.

Well, more than half of this chapter remains, but this is where my quoting stops. The rest of the chapter deals with Clark's spaceship and the construction of his Fortress of Solitude in the Arctic, just like we saw it happen in Superman Returns, and in Superman the Movie too, if I remember things correctly. And I've got a confession to make, Rachel. Nowadays, after so many years as a Superman fan, not too much about Superman that doesn't have a lot to do with his relationship with Lois interests me anymore. Oh, it was totally appropriate and perfect to have his Fortress created in your story, too, but... well, the details don't interest me.

I keep thinking about Jor-El, though. I don't much like the Jor-el in this story. Okay. I guess I wasn't done quoting after all.

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“If your arrival on Earth proceeded according to plan, you have known of your Krypton heritage since the year of your ninth-Earthly birthday, approximately six years after you arrival to that planet. Now you should be nearly grown—a young man approaching manhood, and this fortress is designed to guide you on that journey—to your destiny.”
Disgusting! Talk about laying out your son's life for him before he has a chance to live it on his own.

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“We have recorded the knowledge of the 38 known galaxies in the crystals before you,” his father continued, heedless of his son’s thoughts—of course. He was dead. This was like a film, a movie—a last recording, like the globe was. “For the next eight years of your life you will learn from them. And then you will be ready.”
That talk about 38 known galaxis, which is taken straight from Superman Returns, is nonsense, I want to point out. Humanity has a reasonable knowledge about thousands of galaxies, but that doesn't mean that our knowledge about all these galaxies, including our own, isn't still rudimentary. If the Kryptonians, unlike us Earthlings, had such complete knowledge about 38 galaxies (and why only 38? And which ones, I wonder? The Large and Small Magellanic Clouds? The Andromeda Galaxy? The Sculptor Dwarf? Messier 81 and 82? IC 342? Maffei 1? NGC 253? The Virgo cluster galaxies?) then how could they remain so ignorant about the fate of their own planet that they couldn't even save themselves by escaping to one of these other galaxies which they must have had such perfect access to? The 38 known galaxies - what nonsense.

Ah, but - that infuriating Jor-el! I have barely stopped fuming at his nonsensical talk about galaxies than I see red at the way he wants to rule his son's life from beyond the grave.

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Ready? Ready for what? And destiny? What end had his father meant him for?

To rule over them, but never as a tyrant. That was what the globe had said, anyway. But how literal had his father meant it?
No matter how figuratively he meant it, it was too literal for me. mad

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Clark shook his head. The idea wasn’t even chilling to him—it was just laughable, in a grim sort of way. He had no desire or right to rule over Earth—as a tyrant or otherwise. Technically, he couldn’t even run for president.

Besides, he was Clark Kent. He didn’t want to rule over anybody.
I was in London last week, and I and my friend went to the National Portrait Gallery. I'll never forget the incredibly moving painting of the little King, Edward VI, looking all of his nine years when he was made King of England after his fearsome father's, Henry VIII's, death. I can just imagine all the plans his imposing father had made for his little son. But the poor boy died himself at sixteen.

Gaaaahhh! Jor-el doesn't understand his son at all. Clark is gentle, loving, sincere, altruistic, noble, hopelessly in love with Lois, and a little scared. Clark is not cut out to be anybody's ruler. And Jor-El is dead. Please make Clark understand that he shouldn't listen too much to Jor-el, irrespective of the fact that Jor-El and Lara were the two people who once gave Clark life.

Fascinating chapter, Rachel, but I hope to see a lot of Lois next time.

Ann