My, but they're in a predicament. What will Lana think of this? "Not only does she sleep naked with him, she puts him in mortal danger! She's insane!" Or Joe? "You won't sleep with me but you'll go flying in a cargo hold with him?" And in light of the recent agreement between Joe and Lois, he might conclude that being around her isn't all it's cracked up to be and it would be best for his sanity if they split up.
I think that Clark will be forced to use his "special abilities" to get them out of this fix and Lois will call him on it. She'll press for the whole story and he'll give her just enough to make her even more curious, but she'll convince him that despite the story potential, she'll keep the secret. And she'll probably even give him co-writer credit on the story.
I wonder about Sam's girlfriend. Is she in this willingly? Has she been forced into this? Or maybe is she in it with Sam and has been pushing Lois away so Lois won't learn the nasty truth about her father? Is she doing this out of some loyalty (misguided or otherwise)? And where are the guns going? Are they criminals or patriots? Are they in it for the money or are they driven by ideology? The answers will make a difference in how Clark and Lois are treated when they're discovered.
And I think that if Clark ever gets back to calm with Lana and tells her about any of his powers she's going to freak out. She'll get sick at the very thought of making out with an alien or a mutant or a genetic disaster. I doubt she'll take it well.
Neat story twist, and except for the A-plot warning you gave, it took me by surprise. Of course, that's why we saw all those questions about aircraft cargo holds not long ago. Sneaky and clever, you are. And a very compelling story you present, also. Keep it coming, you must!