I do have to guess this, it's so waffy! "The scream" by Christiane Schmidt.

Quote
And that's when she figured it out: the secret. She wasn't quite
sure how she could have been so blind, so oblivious, but her conversations
with Amanda triggered something. Lee had traveled all over the world. Lee
was fluent in all sorts of languages. Lee came and went inexplicably. It
was a pattern Lois knew all too well. Clark disappeared at the drop of a
hat. Clark could order dinner in 347 languages. Clark had traveled
extensively... England, France, China and who goes to work for the Borneo
Gazette as training to be a serious journalist? These were all clues she,
Lois Lane, had missed. It was all an elaborate cover. She didn't know who
exactly he worked for, whether the CIA or the FBI or the... the... the RTD,
DMV, MTV... whatever those silly government alphabet initials were these
days, Clark was a spy!
laugh

Ok, this is the real cluechie part, same story:

Quote
"Thanks," he gasped out. "I'm feeling better, just weak." He took
the canteen and poured a little out into his palm, rubbing his neck,
letting the liquid flow down his back.
Lois dumped out the contents of her pack onto the ground, searching
for anything else that might help. "You were fine before we went in there,
I just don't understand. What is it you need?"
Clark sighed loudly. "Lois, I'll be fine in a few minutes. I just
can't go back in, not with the Kryptonite in there." He'd taken off his
glasses to rub the water over his forehead and over his eyes.
"That doesn't make any sense, Clark. There's only one person that
stuff affects and..." Lois stopped dead as she turned towards him, staring
at his naked face, hair slicked back from the moisture. Her mouth dropped
open and her knees seemed to buckle right out from under her.
Simona smile