That's The Hand that Rocks by Christy Landrum.

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Quote
"Clark?" she asked quietly.

He pulled her into a tight embrace and whispered into her ear. "They have
this place bugged."

For a moment Lois shrank into Clark's embrace, looking blindly around as if
to see the armies of roaches and rats which were surely waiting in the
darkness.

Then she relaxed, finally getting his meaning. It was a sign of the pain she
was in that she was so slow on the uptake. Usually she was a step or two
ahead of everyone else, and it was all Clark could do to keep up with her.

She whispered in his ear. "They have Kryptonite bullets. We have to get out
of here... and warn Superman."

Lois obviously wasn't sure about how sharp the microphones were, and was
playing her bets safe.

If she had to move heaven and Earth, perhaps come back to haunt Perry and explain the story after they'd killed her, she would do it.

Waking a Miracle by Aria