There's one I've read, I think here or on Big Apricot, which starts out with Superman as a government-controlled, sinister, and very secret super-agent who happens to rescue Perry as part of a mission, then years later breaks free of government control and becomes Clark, I think as a result of having met Perry but I could be wrong.
Marcus, I think the story you're thinking about is Dandello's excellent (and very chilling)
"Ubermann" .
I just re-read it. Actually, "Clark's" motivations for assuming the "Clark Kent" identity are a little different than the way you're making it sound, but Perry is involved.
Highly recommended.
