The series that comes to my mind is "The Saga Continues" by Joel Schudt. There were several parts, and I found it a really interesting series. (I beta-read the first handful of them.) In this series, our Clark and Alt Clark team up to stop an evil Lord Kal-El (from yet another universe) who is working with our Lex Luthor.

There is another story niggling at the back of my mind, though, but I can't seem to come up with an author or title for it ... I seem to remember a story where Lois is a freedom fighter in a Metropolis that has been taken over by the New Kryptonians, possibly led by Lord Kal-El. But I can't recall much more than that ... I think I might have beta-read it, or the beginning of it, and it was years ago ...

OH! Wait, I think I found it ... looking, looking ... yay!

Is it "The Darkness Within" by Lyds?

Quote
Clark Kent becomes trapped in a world where the dark Lord Kal-El has left Metropolis in tatters, and Lois running for her life. Clark must find a way to correct a horrible wrong and bring Luthor to justice.
http://lcfanfic.com/stories2/darkness.txt

Archive says it was a Kerth nominee in 1999. smile

Kathy (who is feeling extremely proud of herself for coming up with this story, considering it came out in 1998. The little hamster was working overtime on the wheel in my mind, believe me! I can't believe I actually was able to remember enough to go looking for it. <g>)