Another excellent part! Wow, things are really starting to happen.

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“I’m not here to answer your questions, Mr. Kent. I’m here for answers. Now, where can I find the alien?”

There is a tense moment of silence before Clark pulls his wide eyes away from the box to rest on Trask’s malevolent face. From across the room, I can see him swallow roughly and when he speaks, his voice is hesitant and tense.

“S..superman has never said where he lives. H…how could I tell you?”

“I don’t think he has to tell you. I think you already know. Have you been harboring the dangerous alien all these years, helping to deceive us and lull us in to a false sense of security before the attack?”

“There is nothing dangerous about Superman. He’s only trying to help!”

“Where can I find the alien?”

Clark says nothing, but reiterates his earlier answer with a simple shrug of the shoulders. Trask’s eyes narrow before he tries another tactic.

“Where did the alien come from?”

“I don’t know.” Clark mumbles.

“How did it get its powers?”

“I don’t know.”

“Are there others like him?”

“I don’t know!”

“Tell me the timeframe for the invasion.”

“There is no invasion! As far as I know Superman is alone. He only wants to use his powers to save lives and make the world a better place.” Clark yells, his face flushing with frustration at each provocative question.
I love this part. As far as Trask, the soldiers, and Lois know, Clark is talking about Superman, a separate person. And yet we know Clark is talking about himself and telling the absolute truth.

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“Mrs. Luthor. I wonder…what brings you from Metropolis?”

“I’m a big Giants fan.”
Snappy comeback! I love Lois.

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“Are you crazy?” I ask. “You have a radioactive rock that can theoretically hurt a super-powered, invulnerable alien and we’re not supposed to be afraid of it? If that can hurt Superman, just think what kind of damage it can do to a mere human.”
Ah, Lois! You just saved Clark! Another issue: since this fic is from Lois's POV, we don't know if Clark has come across kryptonite before. Did the same thing happen, with the tree falling down? Or is this the first time Clark has encountered green K, a nasty surprise to him? I hope that you can tell us later on in the fic.

Also, are his powers on the fritz right now? Or, thanks to Lois, was the exposure short enough that his loss of power was minuscule?

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I see Clark eye the metal case and he foolishly moves toward the box when Trask cocks his gun, training it on Clark’s forehead....Trask sprints out the open door and disappears down the back stairs at the same time I hear footsteps pounding up the front.
I'm assuming that Trask takes the box with him. But, when you upload this fic to the archive, could you please make that clear? Even though it makes sense for Trask to take the box, I'm left with a little niggling question about, "Well, maybe he forgot it in the rush." And yes, I know that's lame.

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I shake my head at his foolhardy behavior. Even I’m not crazy enough to follow an armed military man without a plan of attack. I almost snort at the thought. Actually, that sounds exactly like something I’d do.
I love Lois. Again.

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I look up into Clark’s face and his expression halts my frantic motions. The way he holds himself speaks volumes; he’s radiating tension and indecision, like he wants to be somewhere else, but doesn’t want to leave me alone either. Instinctively, I know that if not for me, he’d be gone already, probably knee deep in research.
Uh, Lois....maybe knee-deep in research....but maybe, just maybe, flying around out there? Maybe trying to get that box of kryptonite into "protective custody" (which sounds so much better than stealing it from Trask, because we know that Superman doesn't steal.)

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“This is more your story than mine,” I admit. “I’ve been itching to find out what these guys are up to for days, since I first saw them tailing you. I want to expose Trask, but I don’t want to walk over you to do it. What would you say to a joint investigation?”
Oh, excellent! First, you give a very plausible reason why Lois would want to join up with Clark ("Trask is the perfect distraction"). And now from Clark's point of view:

Con: Lois is smart, and if she hangs around me too long she's likely to figure out the secret.

Pro: She's a world-renowned journalist who can help me figure out Trask. And she's not affected by the kryptonite - I already feel like I can trust her, and if I need her to handle the kryptonite she can do it. And, she fascinates me, and I fell in love with her at first sight. Sure! Anything that keeps Lois around me is great!

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The thrill I get when I imagining my name on a newspaper byline again is exhilarating, but it has nothing on the rush I get from Clark’s smile and the touch of his hand.
Ooh...the romance is starting. Now if we can just get Lex in prison and Trask taken care of....there's lots of obstacles yet for our doughty pair!

Your fic is really holding my interest. Well written, good plot, excellent characterization, sly humor at the complications of the secret identity - it's got it all!

Please post more soon.